Deal with future publication DOI and model's DOI + poublications have a license asigned to the materials of the paper. How does this work with the license given to the model? Also, when you update the model docuimentation with the reference to an accepted publication, a new version of the model is given and thus, a new DOI, which is not in the publication (There's the link and the ID to the model but still could be a potential source of missunderstandings).(ESTI)
Time out during the upload https://zenodo.org/record/7380172/files/rdf.yaml (Please DO NOT UPLOAD THIS MODEL)(ESTI)
update workflow RDF

Dec. 7th 2022
Attendees

Name
affiliation
username (github)

Wei Ouyang
KTH
@oeway

Estibaliz Gómez
IGC
@esgomezm

Ivan Estevez Albuja
UC3M
@ivan-ea

Lucia Moya
UC3M
@lmoyasans

Joran Deschamps
HT
@jdeschamps

Fynn Beuttenmüller
EMBL
@fynnbe

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Florian Jug
HT
@fjug

Arrate Muñoz Barrutia
UC3M
@arratemunoz

Pete Bankhead
UoE
@petebankhead

Agenda

bioimageio-core-java library and future versions of TensorFlow&PyTorch. How is the update?(ESTI)

Ask Carlos
TF model format guarantees: https://www.tensorflow.org/guide/versions#compatibility_of_savedmodels_graphs_and_checkpoints

Uploads of models in Zenodo that are not published in the zoo: anyone can upload it (https://zenodo.org/record/7380172/files/rdf.yaml) without being the owner(ESTI)

No because the owner needs to give access to the bioimageio community to the repo of zenodo

Deal with future publication DOI and model's DOI + poublications have a license asigned to the materials of the paper. How does this work with the license given to the model? Also, when you update the model docuimentation with the reference to an accepted publication, a new version of the model is given and thus, a new DOI, which is not in the publication (There's the link and the ID to the model but still could be a potential source of missunderstandings).(ESTI)

We don't believe that people will cite the model DOI instead of the publication
Citing "wrongly" the bioimage model zoo rather than the model being published
Relationship of the publications to cite (model zoo + used tool (qupath, imjoy, ilastik, deepimagej etc.) + related publication). We're fully aware that we need to educate users and properly document on the zoo to know how to cite correctly.

Next consortium meeting. Rachel: short presentation for which type of events + what's the budget we have.

Java hackathon, tomorrow the invitations will be sent

Bea: with galaxy they use matrix elements that's an alternative to Slack. Gitter rooms are also matrixable. It has a slack bridge so every room/channel can be connected. We are moving to Matrix elements. For this, send the user name to

update on workflow RDF

quick hypha question: how to avoid timeout?

Question about CI: do partners need to do static validation?

depends: if they require a specific version (potentially auto-updated to) then that might make sense. In general the collection CI does static validation which should be sufficient.

QuPath release + Bioimage Model Zoo extension

https://github.com/qupath/qupath-bioimageio-spec/blob/main/src/main/java/qupath/bioimageio/spec/BioimageIoSpec.java

Rebuttal:

QuPath info in the paper could be updated. Docs on bioimage model zoo extension for qupath https://qupath.readthedocs.io/en/0.4/docs/deep/bioimage.html

QuPath info in the paper could be updated. Docs on bioimage model zoo extension for qupath https://qupath.readthedocs.io/en/0.4/docs/deep/bioimage.html (does depend upon snakeyaml, gson and slf4j… can probably remove gson with a bit more work)

There is no Doc on the Java library:

Mention in the publication that there is some doc for the Java library. We could have a very short pitch and linked it to the online doc and the documentation does not need to be ready at the moment of the publication but keep growing.
Suggest GitHub.IO page for example this one https://imjoy-team.github.io/imjoy-docs/. Everything for developers can be linked in the wiki.
The backbone of the doc should be there before we resubmit the paper.

For general documentation, authors can choose where to put their info an linked it.

BioEngine updates: https://slides.imjoy.io/?slides=https://raw.githubusercontent.com/oeway/slides/master/2022/loci.md#/25

Jan. 11th 2023
Attendees

Name
affiliation
username (github)

Florian Jug
HT
@fjug

Wei Ouyang
KTH
@oeway

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Constantin Pape
EMBL
@constantinpape

Anna Kreshuk
EMBL
@akreshuk

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Ivan Estevez Albuja
UC3M
@ivan-ea

Joran Deschamps
HT
@jdeschamps

Arrate Muñoz Barrutia
UC3M
@arratemunoz

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Agenda

Upcoming Java hackathon @ HT Milano
Model Zoo Paper rebuttal

we should have a checkable todo list in the above linked gdoc and assign responsibilities to individuals via gdoc comments and assigning those...

Author list updates...

Email will be sent by Anna and everybody should be ready to speak up.

Sneak-peak: Carlos, Joran, Jean-Yves Tinevez, Stephane Dallongeville, Jean-Christophe Olivo-Marin

Code of Conduct: https://bioimage.io/docs/#/CODE_OF_CONDUCT

We should involve Rachel (via email)

BioEngine Server for test run in the model zoo

using a local server in Stockhol right now
deNBI k8s cluster needs some more fix
We are getting some free Google Cloud credits from NVIDIA, Craig will test it

Florian: AI4Life co-branded DL EMBO course in 2024

Jan. 18th 2023
Attendees

Name
affiliation
username (github)

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Constantin Pape
EMBL
@constantinpape

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Ivan Estevez Albuja
UC3M
@ivan-ea

Joran Deschamps
HT
@jdeschamps

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Lucia Moya
UC3M
@lmoyasans

Carlos García
Pasteur
@carlosuc3m

Ilya Belevich
Uni. Helsinki
@ajaxels

Agenda

Introducing Microscopy Image Browser

Deep MIB: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008374
Deep learning in microscopy image browser
Deep MIB joining the modelzoo
Written in matlab
Weights: ONNx or tensorflow (saved bundled model).
They support model training: choose a workflow (3D semmantic, patch processing) + an architecture. Fix the set of parameters. Training + inference in the same software package.
They could be connected with clusters (still needs to be fixed) and local GPUs
They can continue training from previous steps or load a pretrained model.
First action point: try running one of the models exported from MIB in python  using one of our supported weight formats. (Without going through the whole process of wrapping model in our yaml format)

Ilya will create an issue with short description and a link to the model on bioimage.io: https://github.com/bioimage-io/bioimage.io

Next action point: support modelzoo format in MIB

format description: https://bioimage.io/docs/#/contribute_models/README

Reach out to https://github.com/kaczmarj/wsinfer see this issue

Postponed till Wei joins again. (Wei has put this point on the agenda)

CI DeepImageJ

Test summaries 135/164 -- format ok?
Use case 3: HPA Cell Segmentation - no tiff images, incompatible with DeepImageJ
DEFCon - compatible weights with DeepImageJ in yaml (Esti will update it with TensorFlow saved bundeld model)
Action Point: for feedback on the CI format: make a github issue, tag Fin in there! (https://github.com/bioimage-io/collection-bioimage-io/issues/515)
For the use-case 3 models: missing the DeepImageJ config. Ping Wei about it.

Videos: rebuttal and wait for Beatriz and Florian (Rebuttal status)

Esti shared the videos with Florian and someone from EuroBioimaging for prettifying
Recording the new videos is WIP
More documentation for running models in zero cost is there

site.config.json in bioimageio repository: software vs method

correct tab is application

State of the Pytorch models that need re-upload

ping Anna about this

Is the Bioimage.io collections yaml still the refenrece for the models in the zoo? (https://github.com/bioimage-io/collection-bioimage-io/blob/gh-pages/rdf.yaml)

Jan. 25th 2023
Attendees

Name
affiliation
username (github)

Ivan Estevez Albuja
UC3M
@ivan-ea

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Lucia Moya
UC3M
@lmoyasans

Fynn Beuttenmüller
EMBL
@fynnbe

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Carlos García
Pasteur
@carlosuc3m

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Agenda

Remove status in the resource.yaml. (@esgomezm : opens the discussion in slack/github issue): https://github.com/bioimage-io/collection-bioimage-io/issues/522
Approve the "Cell segmentation in plant tissue" model in the BioImage.IO zenodo community. (@oeway )
Do models with 'runmode: deepimagej' pass static validation? (They should!?! .. And do! :+1:)
update on deepimagej CI (@ivan-ea ): one last step finished soon: writing test summary from actual/expteced image comparison.
Next steps:

run new CI in  deepimagej/models repo (@ivan-ea )
make sure generated deepimagej test summaries find their way to bioimage.io (@FynnBe )

Feb. 1st 2023
Attendees

Name
affiliation
username (github)

Wei Ouyang
KTH
@oeway

Ivan Estevez Albuja
UC3M
@ivan-ea

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Carlos García
Pasteur
@carlosuc3m

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Agenda

quick question to improve bioimageio.spec reliability: add animal nicknames statically to bioimageio.spec Python package with a command to update?

currently we fetch the animal nicknames dynamically on import, which is not always desirable, see spec-bioimage-io/issues/490
analog for tag categories (used only for warnings)
suggested solution: add as static data to spec package, copying to a .bioimageio user folder where it can be updated

Link to the CI github repository. @FynnBe Please link the test summary generated by the deep image repo to the collection repo.
Discuss the Code of Conduct and the committee in our next AI4Life steering committee meeting. (Caterina can also help)
@FynnBe was working in the imjoy-rpc integration of the bioengine. We need to discuss about the state of the pre&post-processing during the HT hackathon.
Paper rebuttal discussion in the Matrix channel: "private-nm-revision"
BMZ at EMBL microscopy course: https://www.ebi.ac.uk/training/events/microscopy-data-analysis-0

Feb. 15th 2023
Attendees

Name
affiliation
username (github)

Ivan Estevez Albuja
UC3M
@ivan-ea

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Carlos García
Pasteur
@carlosuc3m

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Arrate Muñoz
UC3M
@arratemunoz

Florian Jug
HT
@fjug

Constantin Pape
EMBL
@constantinpape

Agenda
last week:

Remove status in the resource.yaml. (Esti: opens the discussion in slack/github issue): https://github.com/bioimage-io/collection-bioimage-io/issues/522

Approve the "Cell segmentation in plant tissue" model in the BioImage.IO zenodo community. (Wei)

Do models with 'runmode: deepimagej' pass static validation? (They should!?! .. And do! :+1:)

update on deepimagej CI (Ivan): one last step finished soon: writing test summary from actual/expteced image comparison.
Next steps:

run new CI in  deepimagej/models repo (Ivan)
make sure generated deepimagej test summaries find their way to bioimage.io (Fynn)

Notes from the HT hackathon

General update: running python from within Java / ImageJ
Workable solution: use Carlos library as the general functionality to run BioIO models in Fiji

Needs to be deployed via Update sites:

ModelRunner = general java library

extra update sites for frameworks (pytorch, tf, etc.) <- this should work under the hood without that the user needs to worry / restart Fiji

Running models on big data in Java (Tischi, Saalfeld, Jean-Yves, Pietzsch)
Currently some information needed for selecting the correct engine does not exist in all models. Especially the framework version, e.g. tensorflow 1.14, 2.4, pytorch 1.11, 2.0 etc.
Other discussion: Retiring tensorflow v1? Possible solution: archiving tensorflow 1 models (and in the future other versions / libraries that become outdated)
Updates of the model format?

Updates of the shape definitions: https://github.com/bioimage-io/spec-bioimage-io/issues/493#issuecomment-1421167638
Add pixel size in the axes definition in the next spec version, maybe just use the NGFF axes or at least be compatible with it: https://github.com/bioimage-io/spec-bioimage-io/issues/290
Model updates to introduce missing features
In general: what is our process for spec update.

How do we handle the support and request for changes from developers? "developer services?

somehow maps to WPs, there will be people starting in March (and Fynn finishing his thesis and going back to this)

Open call is out now, there will be a "Call-a-thon"

who should we invite for the web image analysis hackathon (Wei)

Hackthon money from AI4Life
Zeiss could also be intersted in this one too
Other web-based tools to invite?

Cytomine
Webknossos
Craig, Matthew

Model consumer and producer hackathons

Zeiss is interested to integrate this with Appeer

What's the state of the revision?

Discussion about deleting a model: https://github.com/bioimage-io/collection-bioimage-io/issues/522

Some models have disappeared from the bioimage.io collection (e.g., Multi-organ Nucleus Segmentation)

BioHackathon 2023 in Barcelona, 30 October-3 November 2023

Feb. 22nd 2023
Attendees

Name
affiliation
username (github)

Ivan Estevez Albuja
UC3M
@ivan-ea

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Carlos García
Pasteur
@carlosuc3m

Joran Deschamps
HT
@jdeschamps

Agenda

DeepImageJ passes the CI. Now there are some models that need to pass the CI. Among others the ones from the usecases.

Mdels from the use cases don't pass the CI

Ehnancer mitochondria has some fails in Ilastik
StarDist passes the CI (except for some little fails in Ilastik). This model is in TF 1 but the current notebook of ZCDL4M is already using >TF2.5 so the model will not run in the current version of the notebook. The current version of StarDist is also failing to export the model with >TF2.5, so should we point to an older version of the notebook or try updating the model?
HPA models: Ivan will prepare the correct IJ macro to send it to Wei, so he can update the models to pass the CI
3D UNet: Cell Segmentation from Membrane Staining for Plan Tissues: we cannot update it as Cristina is the owner of the corresponding zenodo repository (Esti)

DeepImageJ should run with TF 2 next week

Updating ZeroCostDL4Mic to TF2 (3DUNet and 2D UNet) so it can be tested on the new version of deepImageJ.

Technical quesion: Compatibility of spec with Json schema?

interesting to have 1 source of truth for the bioimage.io schemas not only from the python spec library
Could simplify the method of changing the versions of the spec and updating it for consumer softwares

March 1st 2023
Attendees

Name
affiliation
username (github)

Wei Ouyang
KTH
@oeway

Ivan Estevez Albuja
UC3M
@ivan-ea

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Constantin Pape
EMBL
@constantinpape

Anna Kreshuk
EMBL
@akreshuk

Fynn Beuttenmüller
EMBL
@FynnBe

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Carlos García
Pasteur
@carlosuc3m

Arrate Muñoz
UC3M
@arratemunoz

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Agenda

Upload models with newer versions of TensorFlow that are similar to the existing ones but not the same. Which should be the naming convention?

We say that is a version update (we don not say that a new version produces the same results). People can recover the old moodel using the DOI.
In the Bioimageio library, if you use the DOI you can recover any of the old models. The fancy name/id would load the latest version of the model instead.

Removing/Hidding models is very much needed. In some cases we need to updated those models so it would be "removing" in a way that the same name can be used again.

Define the new status "retired" for models that were once accepted. This should allow uploading models with the same name, so by checking the Zeno

New version of deepImageJ with the Java library

CI

Models to check (https://github.com/bioimage-io/collection-bioimage-io/issues/515#issuecomment-1449992881) are the ones listed in the main rdf (.yaml or .json).

Documentation should be udpated.
Do not run on all the models always to avoid running out of credits. Run only on the updated models (it's indicated in the collection).

General status, is it working?

Logic: It sais which frameworks/software have tested the model. For each of the linked software (e.g., deepImageJ and Ilastik), when the test passes, the icon will appear in the "This model can be used in:".

StarDist models with TF1 and TF2:

We do not update the ones from the usecase for now, so they can be still used in Fiji/StarDist as well.

What do we need for the rebuttal?

Updating models

Pytorch models from Adrian (7 models, Constantin will help)
Updated HPA models (@oeway)
DeepImageJ / ZeroCost updates (Esti is uploading it now, need to be then tested in DIJ)
Retiring the 3D u-net model so that esti can push the new version (see the points on model retirement above)

Buttons for partners / software

The "landing page" still needs to be updated for QuPath (Wei has contacted Pete)
The compatibility mechanism would need CI for all partners to be fully functioning

Where are we on this?
Can we have a manual over-ride mechanism? I.e., a partner just gives a list of compatible models instead of the full CI set-up. This would allow us now to go ahead without QuPath and StarDist having to implement CI, and in general would be a good option for smaller software partners that just support a few models.
We have a solution for the  manual over-ride moment: we add the link to the partner in the collection. This can be done by anyone that has write access to the collection. In practice: add the links to the model, e.g. this one: https://github.com/bioimage-io/collection-bioimage-io/blob/main/collection/10.5281/zenodo.5764892/resource.yaml#L19-L23
Another alternative: The partners generate only the test summaries for the models they choose (without having CI).

partners would only need a repository with a gh-pages brach with the test summaries in the correct folder structure.

Fixing the download numbers: hard to solve with zenodo, could instead be solved with google analytics (lawyer says not a good idea, for privacy reasons?).

Is there an alternative compatible with GPPR? matomo?! https://matomo.org/ @oeway
Hide download numbers for now?!
Can we use minimal Google Analytics and raise a disclaimer to be GDPR compliant?

How to fine-tune a model with ZeroCostDL4Mic: link the models to the documentation and whenever there's a video, to the video.

Test run button is not working reliably either in Chrome or in Firefox (it should be tested)
The problem seems to be mostly out of memory issues and sometimes that models cannot be loaded from zenodo @oeway

Code-of-coduct (will be shared in matrix)

Add Icy as a partner (https://github.com/bioimage-io/collection-bioimage-io/pull/543)

Videos:

Video 1 (model upload final cut): https://oc.embl.de/index.php/s/JBWwJGgsXh0vYM6
Video 2 (model compat final take): https://oc.embl.de/index.php/s/eJOIdzDVJpToETd
Video 3 (model zoo test run): https://oc.embl.de/index.php/s/y5wlE08YRGBgtOs
Video 4 (model zoo video compatibility): https://oc.embl.de/index.php/s/NAEFeuWjkwUDlTR

March 8th 2023
Attendees

Name
affiliation
username (github)

Ivan Estevez Albuja
UC3M
@ivan-ea

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Constantin Pape
EMBL
@constantinpape

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Wei Ouyang
KTH
@oeway

Arrate Muñoz
UC3M
@arratemunoz

Agenda

Technical work for the revision

model updates:

pytorch / torchscript udates are done
there are some which have issues in DeepImageJ, but that needs to be checked on the DIJ site first
missing: HPA model (cell segmentation) from Wei, which is updated in zenodo, but not on the modelzoo yet
what about tf2 models

models exported from zero-cost work in Fiji, but don't work in the stardist library (depending on the tensorflow version) -> need to ping Uwe and Martin, we shouldn't delay the rebuttal for this, tensorflow version chaos

QuPath is joining as community partner, but

one of the figures may change, because we can now run it in QuPath easier

let's ask Pete if he can send us the corresponding screenshot in the new QuPath version
and we also keep Florian in the loop because he assembled the figures

bioimage.io

community partners

why is bioimage.io in the partner list on the website -> let's remove it, @Wei
list of the "real" community partners, including a list of their webpages

what about fiji?
what about stardist (we should add it)

the list of partners can be added to the doc here: https://bioimage.io/docs/#/community_partners/README, @Caterina
similar questions for AI4Life: https://ai4life.eurobioimaging.eu/about-us/#part

clarify the relation between community partners in bioimage.io and AI4Life

WP3 and contact form (on bioimage.io website) -> @Wei will add Caterina there
joining image.sc with bioimage.io

who asks and who is added as a community partner? -> Caterina, we can extend the monitoring team as needed
to join: write a post on image.sc

here's the related FAQ: https://forum.image.sc/t/frequently-asked-questions/18729
here's MoBIE as an example: https://forum.image.sc/t/mobie-wants-to-join-as-a-community-partner/68148

Code of Conduct committee:

Anna, Fynn, Roberto and Caterina are the ones in now
It should be an odd number, maybe someone external
There should be a contact person out of the committee

Promotion

Follow ai4life and everyone on tw, linkedin and everywhere please!
Download Element Matrix if you haven't

March 15th 2023
Attendees

Name
affiliation
username (github)

Ivan Estevez Albuja
UC3M
@ivan-ea

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Wei Ouyang
KTH
@oeway

Arrate Muñoz
UC3M
@arratemunoz

Iván Hidalgo
IGC
@IvanHCenalmor

Fynn Beuttenmüller
EMBL
@FynnBe

Agenda

Welcome to new member! @IvanHCenalmor

add to the mailing list?
enrollment procedure for AI4Life? Fill out [this form].(https://docs.google.com/forms/d/e/1FAIpQLSfJNi_H1rKARkGQK9J0WHje9I4_pMZeNNDusAb4gprlcUx75g/viewform)

Where can I find the BMZ logo?

expected it here: https://github.com/bioimage-io/bioimage.io/tree/main/public/static/icons
found it here: https://github.com/bioimage-io/bioimage.io/tree/main/public/static/img

add AI4Life and Image.SC icons (done!): https://github.com/bioimage-io/bioimage.io/commit/8a1bd04b86da51d24eadb80f8c71dc14e8f80aca
Procedure to onboard community partners
Timeline for BioImage.IO workflows

lets revisit in a few weeks
discuss relation to run_mode

Feel free to join the Hackathon in Stockholm (upcoming hackathon titled "Web and Cloud Infrastructure for AI-Powered BioImage Analysis" which will be held on June 5th-9th, 2023 (5 days), at Science for Life Laboratory, Stockholm, Sweden)

Left for next meeting:

Enable Tracking? -> https://github.com/bioimage-io/spec-bioimage-io/pull/504

March 22nd 2023
Attendees

Name
affiliation
username (github)

Ivan Estevez Albuja
UC3M
@ivan-ea

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Iván Hidalgo
IGC
@IvanHCenalmor

Fynn Beuttenmüller
EMBL
@FynnBe

Joran Deschamps
HT
@jdeschamps

Carlos García
Pasteur
@carlosuc3m

Agenda

Social Media

Follow @deepImageJ on twitter!
Who has the @bioimageio twitter credentials? It is stated on WP3 that we should be tweeting and answering users from that twitter account.

Wei is sharing the co-admin for the tw.

As icy is joining as community partner, they should do some noise from their twitter account @Icy_BioImaging. RTs are promised.

Compile manifest ZeroCostDL4Mic to process the resources in the manifest yaml (it is looking at https://raw.githubusercontent.com/bioimage-io/bioimage-io-models/master/utils/compile_model_manifest.py but no longer exists)

We can use the validator from QuPath (spec validator - static).
Example in QuPath already.

Images on https://bioimage.io/docs/#/usecase1stardist are not loading.

dedicated issue created: https://github.com/bioimage-io/bioimage.io/issues/341
@oeway
@egomez

Paper:

deepImageJ official release scheduled for the 11th of April but we can play with it next week for the CI.
We need to share it with StarDist team so they can test it.
deepImageJ will be available for a shy testing before the official release.

Training

Add info about upcoming courses in the AI4Life page.
Everyone add their upcoming events/courses to the AI4Life Training doc

🎉QuPath joined as new community partner： https://bioimage.io/#/?partner=qupath&type=all

New community partners info

https://github.com/bioimage-io/bioimage.io/pull/340

issue about navigating the docs: https://github.com/bioimage-io/bioimage.io/issues/339

March 29th 2023
Attendees

Name
affiliation
username (github)

Ivan Estevez Albuja
UC3M
@ivan-ea

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Iván Hidalgo
IGC
@IvanHCenalmor

Joran Deschamps
HT
@jdeschamps

Carlos García
Pasteur
@carlosuc3m

Constantin Pape
Uni Goettingen
@constantinpape

Florian Jug
HT
@fjug

Wei Ouyang
KTH
@oeway

Anna Kreshuk
EMBL
@akreshuk

Arrate Muñoz
UC3M
@arratemunoz

Beatriz Serrano-Solano
Euro-BioImaging
@BeatrizSerrano

Agenda

MONAI
PANOS meeting:

Interest in the model zoo and open calls from the EM community
Integration with Deep MIB: https://github.com/bioimage-io/bioimage.io/issues/324
Developer hackathon for support with model support

yearly hackathons for this
Hackathon in Heidelberg: could host both the "Solvathon" for OpenCalls and the Developer Hackathon
there is also another Hackathon idea for user facing hackathon

Analytics (download statistics)

Switch to matomo or Plausible.io: https://github.com/bioimage-io/spec-bioimage-io/pull/504
Need to host it ourselves or pay the subscription
Definition of download: count only the download of RDF file
additional rule for community partner (consumer): report download

April 5th 2023
Attendees

Name
affiliation
username (github)

Ivan Estevez Albuja
UC3M
@ivan-ea

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Iván Hidalgo
IGC
@IvanHCenalmor

Joran Deschamps
HT
@jdeschamps

Carlos García
Pasteur
@carlosuc3m

Constantin Pape
Uni Goettingen
@constantinpape

Florian Jug
HT
@fjug

Anna Kreshuk
EMBL
@akreshuk

Arrate Muñoz
UC3M
@arratemunoz

Beatriz Serrano-Solano
Euro-BioImaging
@BeatrizSerrano

Agenda

BioHackathon

End of October in Barcelona
Topic: Fair Image Annotations
Should we expand this to also include Models / BioImage.IO

This means someone should travel.

There seems to be some interest from the BioHackathon Community.
Joining remotely is also possible, and it would

OpenCalls:

72 applications, Florian et al. are prescreening
After April 12th that should be done and then the applications will be distributed to the reviewers.
Solvathons to work on the challenges

I2K 2024: in Milano

April 12th 2023
Attendees

Name
affiliation
username (github)

Ivan Estevez Albuja
UC3M
@ivan-ea

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Iván Hidalgo
IGC
@IvanHCenalmor

Carlos García
Pasteur
@carlosuc3m

Constantin Pape
Uni Goettingen
@constantinpape

Wei Ouyang
KTH
@oeway

Anna Kreshuk
EMBL
@akreshuk

Agenda

Updates from Esti about FOM and MONAI

Interest from the FOM community about uploading new models in Matlab
Ivan is testing models from MONAI

Hakathon in Stockholm:
Converting Segment Anything Model from Meta: https://github.com/facebookresearch/segment-anything
Running BioEngine containers locally
Nature Methods paper

will be finish soon
figures @florian

April 19th 2023
Attendees

Name
affiliation
username (github)

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Iván Hidalgo
IGC
@IvanHCenalmor

Carlos García
Pasteur
@carlosuc3m

Constantin Pape
Uni Goettingen
@constantinpape

Agenda

Paper: Figures (Wei and Constantin)

Resubmission? =)
DeepImageJ will be released in the upcoming days.
Anna will review the text and share with the authors.

MONAI: show the model converted

They create all the models in their zoo (so not really external contrbutions such as in the BMZ). A config file is created to not only define the inference part but also the parameters that define the network architecture that they will load.
They provide a configparses to rescue the metadata of the model. It's straightforward to recover them.
Data recovery (obtain an example image) cannot be done automatically as they provide links
Authors and licenses are different as they claim the authorship and they have their own licensing.
Models converted by Iván: Pathology nuclick annotation adn wholebody ct segmentation models
If we think about a conversor, pre and post-processing may be a bottlenec: What axis do they expect, batch dimension, do they not, what's the input shape
Try to get a translation script either for each of the models (~24) or a general script (this sounds too ambitious). Ideally we could enable life-scientists using monai to retrain - finetune, or use monai more for bioimages rather than medical and populate the zoo with these new trained models. In MONAI they have models as arquitectures rather than as "trained model instances", so what is offered in the BMZ is different from what is offered in MONAI. This would only imply translating monai config (by rataining their config in the zip file) rather than MONAI getting addapted to us. The latter seems quite ambitious at the moment as they need to discuss any new feature with product managers.
Wait to finish the axis definition. They will include the pixel size so then we can run up/down-sampling scripts.
Make a script functional that we can play with (Iván).
Make an issue for the resizing preprocessing step
Put their config in our specs in the config / monai: propose so we wouldn't need to translate them. modelpy automaticall by resolving the inports and then curate them manually.
Iván/Esti will try to get a proposal for a format translator in 2 weeks

CI & Size of the models
It will depend on wether it is Pytorch or Tensorflow. We run on CPU and not on a GPU.
SPECS:

1 hour limit for inference
2-core CPU (x86_64)
7 GB of RAM
14 GB of SSD space
The model validation has never failed so far. For testing workflows it may be a bit more difficult. We should focus on technical test cases rather than the direct application. Reduce it for example, to a reasonable area.

April 26th 2023
Attendees

Name
affiliation
username (github)

Joran Deschamps
HT
@jdeschamps

Iván Hidalgo
IGC
@IvanHCenalmor

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Dominik Kutra
EMBL
@k-dominik

Ivan Estevez Albuja
UC3M
@ivan-ea

Agenda

Introducing Vera and Mehdi!! (Milan) :tada:
Models from MONAI will be passed to the chat so everyone has access to them.
Is the json schema of the spec completle compatible?

ask for the specific problematic fields in an issue

May 3rd 2023
Attendees

Name
affiliation
username (github)

Joran Deschamps
HT
@jdeschamps

Iván Hidalgo
IGC
@IvanHCenalmor

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Ivan Estevez Albuja
UC3M
@ivan-ea

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Florian Jug
HT
@fjug

Constantin Pape
EMBL
@constantinpape

Fynn Beuttenmüller
EMBL
@fynnbe

Carlos García
Pasteur
@carlosuc3m

Arrate Muñoz
UC3M
@arratemunoz

Mehdi Seifi
HT
@mese79

Agenda

Leica AIVIA's BioImage Model Zoo integration. Wei was contacted and they were intrested into knowing wether becoming consumers or produces. See if they can support the format.
Hackathon after Seeing is believing in Heidelberg and 3 days after the general assemnbly.

2 topics: (1) developathon. It would be great to have someone from Zeiss, Leica, make a prototype in their tools. (2) solvathon. Work on the problems chosen in the Open Call.

Deadline Open Call review. Send hopefully tomorrow to reviewers. Given about 10 days-14 days. Every reviewer should go over 15. 3 text fields, multiple choice questions. 15 minutes for one (warning: estimate by Florian... ;).
Monai people presentation status? Wei: "Maybe we can integrate the conversion script of MONAI in the collection CI then automatically make them available in the model zoo?". We can get a general conversor that works for some models but there may be exceptions.

Their format has features for (1) data loading, (2) training, (3) further pre/post-processings

Wei: "Cloud run could be an interesting case, so we can deploy it in the bioengine"

Wei: "Make their library as a consumer, just like stardist/csbdeep?"
Have a dependency list in which we can include their library (Esti: please @Fynn include whatever you want)
There is no need to have a special runmode as they are normal models. With some manual engineering we can convert these models.
In MONAI they accept models as the whole architeture + training rather than trained instances or models (like in the BMZ). So this is kind of the mutual benefit. Wei: "Yes, that’s a good idea! so in that case MONAI can be only consumer(as a start). In the future we can ask them to integrate a export and upload to BMZ feature in their library so their user can stream models to the model zoo".

Next wednesday: NEUBIAS + lab retreats
SAM: Constantin has been working on something, will probably make it public next week

May 10th 2023
Attendees

Name
affiliation
username (github)

Iván Hidalgo
IGC
@IvanHCenalmor

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Fynn Beuttenmüller
EMBL
@fynnbe

Carlos García
Pasteur
@carlosuc3m

Wei Ouyang
KTH
@oeway

Anna Kreshuk
EMBL
@akreshuk

Agenda

Monai update

axes update issue: https://github.com/bioimage-io/spec-bioimage-io/issues/290

check SHA256 integrity in bioimageio.core dynamic validation

Future Topics

General meeting in October

May 17th 2023
Attendees

Name
affiliation
username (github)

Iván Hidalgo
IGC
@IvanHCenalmor

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Fynn Beuttenmüller
EMBL
@fynnbe

Carlos García
Pasteur
@carlosuc3m

Wei Ouyang
KTH
@oeway

Anna Kreshuk
EMBL
@akreshuk

Agenda

Monai update

axes update issue: https://github.com/bioimage-io/spec-bioimage-io/issues/290

check SHA256 integrity in bioimageio.core dynamic validation

BioImage.IO Meeting Minutes
May 17th 2023
Attendees

Name
affiliation
username (github)

Iván Hidalgo
IGC
@IvanHCenalmor

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Fynn Beuttenmüller
EMBL
@fynnbe

Carlos García
Pasteur
@carlosuc3m

Wei Ouyang
KTH
@oeway

Anna Kreshuk
EMBL
@akreshuk

Ivan Estevez Albuja
UC3M
@ivan-ea

Beatriz Serrano-Solano
Euro-BioImaging
@BeatrizSerrano

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Arrate Muñoz
UC3M
@arratemunoz

Plus people from NFDI4DataScience

Agenda

NFDI4DataScience is joining today!

They are interested in getting the metadata associated to the models to be linked from the portal they are building
They are using https://bioschemas.org/
Summary of recommendations after the workshop on image data annotations (AI4Life, WP5): https://zenodo.org/record/7681687#.ZGTjr-xBwsc
Challenges: https://www.nfdi4datascience.de/docs/community-engagement/shared-tasks/
We can organise a workshop together (involving Bioschemas and EDAM)

NEUBIAS Updates

Basic knowledge to be able to get in touch with the zoo: notebooks, models, etc
Searching. Could we improve its functionality?

Can we get (more) fuzzy search?

Dictionary for icons on the model's card
Most questions: how can I upload a model? What do I need? What is there that I can use to upload a model?
How do we fill the gap?

Proposal from Esti: Have three VERY BASIC notebooks (tensorflow, ONNX, Pytorch) that shows how to export a model and get the zip file.

May 24th 2023
Attendees

Name
affiliation
username (github)

Iván Hidalgo
IGC
@IvanHCenalmor

Wei Ouyang
KTH
@oeway

Beatriz Serrano-Solano
Euro-BioImaging
@BeatrizSerrano

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Arrate Muñoz
UC3M
@arratemunoz

Joran Deschamps
HT
@jdeschamps

Florian Jug
HT
@fjug

Sebastian Rhode
Zeiss AG

Mehdi Seifi
HT
@mese79

Vera
HT

Agenda

Zeiss joining the meeting (in the form of Sebastian Rhode).

Sebastian Soyer is attending the Hackahton in Stockholm
Florian: We discussed for about 1h about what Zeiss is up to with Apeer and how it is similar (or not) to our efforts. Unfortunately, nobody took minutes, but in summary: the hackathon will be a great place to deepen this dicussions.
Problems experienced in Zeiss: same model in different workstations or (their own) platforms do not produce the same results pixelwise (GPUS etc.). A way they have to test this is by either measuring that identified instances are the same or by allowing a threshold for the difference (i.e., error tolerance).
They use containers (containers are industry standard). Open container image format (“pomer”). It allows them to have a separation of concerns: bug on the code, if it’s in the container, then you can fix for everyone. Ensures stability
Couple of training pipelines in place:

1 pipeline for N2V
1 for instance seg
1 semantic seg
1 object classification

TRAINING:

They have a data driven model development: Their training schedule is optimised for the data and is rerally fixed (the user does not have the chance to modify training parameters).
They have training standards

Some of their ideas

Convince users to retraining on a regular basis (not only for a phd project).
Do we have standards for tiling? They do some
Apeer could be a central place where people trains their models.
Researchers won’t use their platform to train models unless they can do it in their platforms, and use the model wherever I want.
Increase the impact of trained models
Users in their micro-communities, they need the same segmentation method.

Options to use Apeer:

Basic version: for free. They will use the data, limiting time, and storage
Yearly subscription probably with a 50% discount for academia.

WHAT CAN WE DO: create a dictionary or translator between their format (JSON) and our (RDF.YAML). They have few pipelines for training only. Once these are translated (4-6), their models will be fully compatible.

Namensvetter - “dude with same name” ;)

Topics for the hackathon:

The bioengine, how the scalable AI model serving is expected to be working
Zenodo failed during the EMBL-EBI course. Proposed alternative to explore: Hugging face (https://huggingface.co/datasets)

May 31st 2023
Attendees

Name
affiliation
username (github)

Iván Hidalgo
IGC
@IvanHCenalmor

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Florian Jug
HT
@fjug

Mehdi Seifi
HT
@mese79

Ivan Estevez Albuja
UC3M
@ivan-ea

Carlos García
Pasteur
@carlosuc3m

Agenda

Status of model download tracking?

Plan to deploy the matomo server to the embassy cloud at EBI. (Wait for the next meeting with Wei)

Status of the java library, how to describe it inside the BMZ manuscript

deprecate the imagej-modelzoo and replace it with the JDLL?
DeepImageJ is able to consume TF2 but it needs to be tested by different OS and users.
JDLL should be released this week or the next one, and after that, deepImageJ 3  can be released. JDDL is in Maven. Carlos is working on the documentation, to see if it's clear and self-explanatory.

Paper:

Few things do not work very reliably. Shall we submit early or should we fix them first before submitting it?
Make a list of features that need to work (plan to do it in the next meeting)

BioEngine does not connect to the last version of the model (Wait for the next meeting with Wei)

Hackathon

Wei sent a link to a doc to the participants to suggest some topics
Propose to use the bioengine as a finetune engineering and maybe CellPose could be a good use case for this.

Translators from other software/packages to the BioImage format

Repos can be in an organisation
Structured in a way that can serve as an example or guideline for a new translator.
How many new people would create their new format and now wouldn't do it because the BMZ exists (this is more our main focus).
Legacy (yes, we have to look at these carefully) but also to future integrations
Tutorial training videos to show how from an existing OS we can easily be more compatible using the BMZ library.

It can be prepared as part of WP3 (AI4Life)

Important point is reproducibility + easy citability.

FocalPlane asked for content. Two chances (1) Blog post is more oriented to discussion and it's shorter. (2) Tool category to explain how to do use it or a use case.

If someone wants to write something (what it is).
Exercises
Selection from the Open Calls (statistics, what are the problems demanding, which one did we demand). Point to the models in the BMZ that have been created to solve these issues.

Doc that states what we expect from consumers&producers (WP4 for developers).

Also important to discuss in the steering committee. What should we put in AI4Life to say what we are and we are not doing.
How they can contact us.

Get more people's hands on the BioEngine, BioImage Model Zoo and all the engineering behind the model zoo.

EGM will join the AI4Life meetings.

Status of automatic tests for new partners (e.g. Icy), can we add icons for them in the test summary? @Carlos for Icy, is the automatic tests working, if not, have you tested the models, maybe add the icons manually in the collection repo for the icy-compatible models for now?

A partner: either produce or consume models
deepIcy: should it be released before the submission? It could be done in a few weeks after the hackathon.

June 7th 2023
(The stockholm hackathon)
Attendees

Name
affiliation
username (github)

Iván Hidalgo
IGC
@IvanHCenalmor

Florian Jug
HT
@fjug

Mehdi Seifi
HT
@mese79

Ivan Estevez Albuja
UC3M
@ivan-ea

Carlos García
Pasteur
@carlosuc3m

Wei Ouyang
KTH
@oeway

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Arrate Muñoz
UC3M
@arratemunoz

Vera Galinova
HT
@veegalinova

Nodar Gogoberidze
Broad Instittue
@gnodar01

Agenda

General meeting in October

Monday lunch to tuesday lunch general meeting
3 days hackathon: bring your PhD student to work!

Op. 1: solvathon: mid-expert people to solve the open call problems
Op. 2: developers hackathon: us + future partners/consumers/producers
Op. 3: do both at the same time

Axes spec in 0.5.0: https://github.com/bioimage-io/spec-bioimage-io/issues/290

hackathon topic: infer task tag from output tensor format
ngff axes discussion: https://github.com/ome/ngff/issues/35

Leica will join and present on 14th June, at 4pm CET.
Difference between being a Consumer/Producer of models and being a Community Partner

Consumer/producer is a contributor of the zoo
Consumer a group, app, individual person, or even ilastik.
Community partner software needs to have a github repo for a CI and be able to produce/consume the models and run the CI. We want to know which models can they run automatically.
Documentation of community partner:

Add on responsibilities the CI for each Community Partner
To check: Is there enough doc to support developers on this? Who would be the best person to draft the doc? Carlos&Ivan?

How to support custom pre/postprocessing,run_mode workflow spec
https://github.com/bioimage-io/collection-bioimage-io/blob/main/collection_rdf_template.yaml
Open source Python library for building bioimage analysis pipelines: https://github.com/danifranco/BiaPy

June 14th 2023
Attendees

Name
affiliation
username (github)

Iván Hidalgo
IGC
@IvanHCenalmor

Mehdi Seifi
HT
@mese79

Ivan Estevez Albuja
UC3M
@ivan-ea

Wei Ouyang
KTH
@oeway

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Vera Galinova
HT
@veegalinova

Constantin Kappel
Leica

Jose Miguel Serra Lleti
Leica

Agenda

Leica presentation

Constantin and Jose from the AVIA team
Title: "Integrating Biozoo in Aivia"
Aivia: data visualization, pixel object classifier, recipes, workflow processors etc.
Python Recipes: https://github.com/AiviaCommunity/PythonForAivia
Aivia model library: https://www.aivia-software.com/model-library
Aivia software: pre/post-processing? Recipies?
Demo of the Aivia software, drag and drop the model to the software and run it.
4-5 models already in the Aivia software
Suggestions (from Wei):

Standard naming: BioImage Model Zoo or bioimage.io models.
Join as community partner?
A converter? CI?
BioEngine integration?
Ingestion of models to the model zoo
Use the config to store custom info

Hackathon updates

June 21st 2023
Attendees

Name
affiliation
username (github)

Wei Ouyang
KTH
@oeway

Iván Hidalgo
IGC
@IvanHCenalmor

Mehdi Seifi
HT
@mese79

Ivan Estevez Albuja
UC3M
@ivan-ea

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Vera Galinova
HT
@veegalinova

Beatriz Serrano-Solano
Euro-BioImaging
@BeatrizSerrano

Anna Kreshuk
EMBL
@akreshuk

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Agenda

Recap of the presentation from Leica
DIJ 3.0 released

with bioimage-io.JDLL as the backend
now tf2 and onnx models work on Fiji, as well as pytorch 2

EOSC Marketplace

Include Wei and Anna in the application

Paper: Java section update (Carlos)

We don't know which partners can run which models.
deepIcy: which models can they run? There is a missmatch between which partners should be displayed in the model card.
At least CI & association of partners should be clear.
Issue for the userfriendliness https://github.com/bioimage-io/bioimage.io/issues/344  @esti break down the issues by tasks and add the followings:

connect the download with the test summary and remove icons.
run model: it's not straightforward how to load data: there is a black box that when we click nothing happens, so then, one would need to read the text. the "select file" is after the text, which sometimes is not visible. The axes option is too technical. It would be nicer to have a demo with the image already open and clicking run. Then you can have a chance to "try with your data". There is an issue with the axes from new images. "This is how we interpret the image. If this is not true, please, correct the axes?"

QuPath as community partner

June 28st 2023
Attendees

Name
affiliation
username (github)

Iván Hidalgo
IGC
@IvanHCenalmor

Mehdi Seifi
HT
@mese79

Ivan Estevez Albuja
UC3M
@ivan-ea

Caterina Fuster Barceló
UC3M
@cfusterbarcelo

Carlos García
Pasteur
@carlosuc3m

Joran Deschamps
HT
@jdeschamps

Agenda

DeepIcy is preparing the CI which is almost done
JDLL + BioEngine is a work in progress that will be done after the CI of DeepIcy
https://github.com/bioimage-io/collection-bioimage-io/issues/506 -> wants to convert from Pytorch format to torchscript.

July 5th 2023
Attendees

Name
affiliation
username (github)

Iván Hidalgo
IGC
@IvanHCenalmor

Mehdi Seifi
HT
@mese79

Ivan Estevez Albuja
UC3M
@ivan-ea

Wei Ouyang
KTH
@oeway

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Agenda

If someone talks about AI4Life, it needs to be added to this docs: https://docs.google.com/spreadsheets/d/1_n-lO1wJAFXpQl-pFyDeHIl2ilP4Vndv6662M-rVCGY/edit#gid=0
Bea asks if there's a screenshot about Leica's software, but Wei has said that is not published (is still in progress).

September 13th 2023
Attendees

Name
affiliation
username (github)

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Iván Hidalgo
IGC
@IvanHCenalmor

Wei Ouyang
KTH
@oeway

Mariana Ferreira
IGC
@mariana-gferreira

Vera Galinova
HT
@veegalinova

Daniel Sage
EPFL
@dasv74

Fynn Beuttemueller
EMBL Heidelberg
@fynnbe

Anna Kreshuk
EMBL
@akreshuk

Florian Jug
HT
@fjug

Carlos García
Pasteur
@carlosuc3m

Constantin Pape
EMBL
@constantinpape

Agenda

Updates on download statistics (cc @Fynn): https://github.com/bioimage-io/collection-bioimage-io/issues/627

The number of downloadings shown in the model cards has been changed. Now it is based on the volume of downloaded data and the unique download from Zenodo (https://help.zenodo.org/faq/#statistics), therefore (even if it is not totally accurate) the number is more realistic and not as high as before.
Also the images shown in the covers in https://bioimage.io have been cached, avoiding the downloading from zenodo and making the number of downloads more realistic.
A potencial new idea is to also count the number of clicks on each model card (appart from the number of downloadings).
idea: group download counts into categories to level the playing field.
Maybe highlight some model (trending, etc...)
Your suggestions for categories here:

named categories

beloved, popular, liked, caught on

stats based

top25%, top50%, top75%
download percent rank (1,2,3... 100)

additional labels

trending (highest increase in 7 days)

Improving test run interface: https://github.com/bioimage-io/bioimage.io/pull/352 (cc @Nanguage and @cfusterbarcelo)

The Try the model section will be included inside the model card.
Switching the cloud infrastructure to google cloud, check data privacy policy of google: https://cloud.google.com/terms

Hackathon in Heidelberg??

TODO: send confirmation email @Bea

Deploy micro-sam in the BioEngine

identify partys invested in spec changes

https://github.com/bioimage-io/JDLL
https://github.com/bioimage-io/core-bioimage-io-python
https://github.com/deepimagej/deepimagej-plugin
https://github.com/HenriquesLab/ZeroCostDL4Mic

For any changes (breaking or non-breaking) in the spec, please use the @spec-dev team to notify. If you would like to be notified, please join the team

authors vs packaged_by

September 20th 2023
Attendees

Name
affiliation
username (github)

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Iván Hidalgo
IGC
@IvanHCenalmor

Wei Ouyang
KTH
@oeway

Mariana Ferreira
IGC
@mariana-gferreira

Arrate Muñoz
UC3M
@arratemunoz

Constantin Pape
EMBL
@constantinpape

Mehdi Seifi
HT
@mese79

Carlos García
Pasteur
@carlosuc3m

Constantin Pape
EMBL
@constantinpape

Agenda

Clarification on how zenodo count downloads and how to differentiate humam, machine and robot: https://github.com/bioimage-io/bioimage.io/issues/353
QuBIC Tuebingen willl join next week: https://uni-tuebingen.de/forschung/forschungsinfrastruktur/zentrum-fuer-quantitative-biologie-qbic/
Some organizational feedback about the hackathon (by @constantinpape)

Financial support for external ? @fjug @akreshuk
@constantinpape cannot join next year if no financial support
Plan hackathons with more time
@Bea add this to the steering committee meeting

Next Meeting

Presentation from QuBIC

September 27th 2023
Attendees

Name
affiliation
username (github)

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Constantin Pape
EMBL
@constantinpape

Iván Hidalgo
IGC
@IvanHCenalmor

Fynn Beuttemueller
EMBL Heidelberg
@fynnbe

Mehdi Seifi
HT
@mese79

Vera Galinova
HT
@veegalinova

Arrate Muñoz
UC3M
@arratemunoz

Agenda

New testing the models on the model card feature! Check it!!!!!

H&E (Stardist H&E Model): we would expect the input data to be shown as RGB. Probably it would be good to render channels = 3 as RGB
For single channel image we would expect grayscale. E.g. for the LiveCELL model, we would expect to see the input as grayscale. (The cmap right now looks like viridis to me).

The statistics on the downloads of the models is going on, with the new statistics there can be see the change of the counting method, but now is more carefully considered. The agent on the CI is no more taken into account in the downloads, what makes it more realistic. After the counting in the BioImage Model Zoo there are:

41 models
42 datasets
54 applications + notebooks (52 applications and 2 notebooks, but many notebooks are tagged as applications)
more stats can be computed with: https://github.com/bioimage-io/collection-bioimage-io/blob/3667df26315b80622ec77c2d73d4008575106952/notebooks/statistics.ipynb

October 4th 2023
Attendees

Name
affiliation
username (github)

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Wei Ouyang
KTH
@oeway

Iván Hidalgo
IGC
@IvanHCenalmor

Mehdi Seifi
HT
@mese79

Vera Galinova
HT
@veegalinova

Arrate Muñoz
UC3M
@arratemunoz

Carlos García
Pasteur
@carlosuc3m

Agenda

Test run feature of the model zoo:

There is no problem on using a local image with the same size, the problem comes when the size of the image is not the expected one (that gives an error).

How to identify fine tuned models?

Provide a way automatically upload finetuned model
All the finetuned model should have the parent field linked to the model it started
We should also encourage uploading the new annotated data to the model zoo so it can enrich our dataset, which is valuable for training larger model.

October 18th 2023
:::info
Time: 4:00PM CET (your timezone)
Where: Zoom Channel
:::
Attendees

Name
affiliation
username (github)

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Wei Ouyang
KTH
@oeway

Iván Hidalgo
IGC
@IvanHCenalmor

Mehdi Seifi
HT
@mese79

Vera Galinova
HT
@veegalinova

Arrate Muñoz
UC3M
@arratemunoz

Carlos García
Pasteur
@carlosuc3m

Jeremy Metz
KTH / Scilifelab
@jmetz

Mariana Ferreira
IGC
@mariana-gferreira

Agenda

WP3 meeting tomorrow.
Add your courses and workshops here, please:

https://docs.google.com/spreadsheets/d/1_n-lO1wJAFXpQl-pFyDeHIl2ilP4Vndv6662M-rVCGY/edit#gid=0

Zenodo and the BioImage Model Zoo

The BioImage Model Zoo was down during the weekend and until monday afternoon.
The upload feature of the BMZ is still down.

Migrating to the new system.
It will be down for at least one or two weeks until the new system is ready.
Have some video/demo showing on how to upload the model directly to zenodo will the upload feature is down > Caterina's going to do it
See this: https://github.com/bioimage-io/collection-bioimage-io/pull/636

November 1st 2023
Attendees

Name
affiliation
username (github)

Iván Hidalgo
IGC
@IvanHCenalmor

Florian Jug
HT
@fjug

Wei Ouyang
KTH
@oeway

Jeremy Metz
KTH
@jmetz

Agenda

Synergy between docker container efforts, instead of creating separate docker containers for each notebook, try to wrap it as a conda-pack file for the environment and provide a model.py file, then it can reuse the models in the BioEngine. Example for a model: https://github.com/bioimage-io/bioengine-model-runner/tree/main/src/bioengine-model-runner And here is the public model repostiroy, with models and also the shared conda environements: https://uk1s3.embassy.ebi.ac.uk/model-repository

November 8th 2023
Attendees

Name
affiliation
username (github)

Iván Hidalgo
IGC
@IvanHCenalmor

Wei Ouyang
KTH
@oeway

Jeremy Metz
KTH
@jmetz

Weize Xu
KTH (visiting)
@Nanguage

Estibaliz Gómez
IGC
@esgomezm

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Mariana Ferreira
IGC
@mariana-gferreira

Arrate Muñoz
UC3M
@arratemunoz

Anna Kreshuk
EMBL
@akreshuk

Agenda

BioImage.IO community google groups

<EMAIL_ADDRESS>will setup automatic notification

Synergy between docker container efforts, instead of creating separate docker containers for each notebook, try to wrap it as a conda-pack file for the environment and provide a model.py file, then it can reuse the models in the BioEngine. Example for a model: https://github.com/bioimage-io/bioengine-model-runner/tree/main/src/bioengine-model-runner And here is the public model repostiroy, with models and also the shared conda environements: https://uk1s3.embassy.ebi.ac.uk/model-repository

Packages which doesn work inside container on mac host system: imagecodecs

BioEngine Desktop

Using podman desktop
Add BioEngine container features

Updates about the core library

Ask @Joran or someone else from @fjug group

Demo for the new test run

Switching to ImageJ.JS interface @Nanguage
Need some changes to be made to support custom shape in the bioengine model runner

paper status

CI for figure out what can run what
Fix the test run
Upload

rdf.yaml naming discussion

Not changing now, postpone the dicision

November 15th 2023
Attendees

Name
affiliation
username (github)

Iván Hidalgo
IGC
@IvanHCenalmor

Estibaliz Gómez
IGC
@esgomezm

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Mariana Ferreira
IGC
@mariana-gferreira

Joran Deschamps
HT
@jdeschamps

Luis Kuhn Cuellar
QBiC-Tübingen
@luiskuhn

Mehdi Seifi
HT
@mese79

Vera Galinova
HT
@veegalinova

Fynn Beuttemueller
EMBL Heidelberg
@fynnbe

Agenda

Presentation from QBiC Tuebingen (Luis Kuhn Cuellar): Quantitative Biology Center

Their goal is to contribute and consume models to the BMZ
mlf-core docs

(Joran) Deep learning specs and recommendations for OME-NGFF

Working group to draft use cases
Assert compatibility of current OME-NGFF specs
Open issue on OME-NGFF
Put out recommendations for DL-specific Zarr data organization

What to do with a model that we know that is wrong?

Delete it?

November 22th 2023
Attendees

Name
affiliation
username (github)

Iván Hidalgo
IGC
@IvanHCenalmor

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Mariana Ferreira
IGC
@mariana-gferreira

Joran Deschamps
HT
@jdeschamps

Mehdi Seifi
HT
@mese79

Vera Galinova
HT
@veegalinova

Jeremy Metz
KTH / Scilifelab
@jmetz

Daniel Franco
DIPC / EHU
@danifranco

Weize Xu
KTH (visting)
@Nanguage

Agenda

Jeremy has been working on a upload/submission webpage/interface.

This can be found on: https://deploy-preview-2--bioimageio-uploader.netlify.app/
There was a problem with the Login, but it might be hypha server that is failing.
The output of the submission is given in an RDF tree style, Joran proposed to show it in a form more user-friendly style.
The feedback to the user from the status is now just a sentence, but it could be nice to have a progressbar with all the checkings.
Submit issues: https://github.com/bioimage-io/bioimageio-uploader/issues

Retake it or close it?: Bioimage.io Issues.

Meta-issue: Website design, Jul 7, 2020 >> close it

The need of having a twitter link for sharing the model in the model card: Share via twitter

The icons in the windows showing the models are inconsistent and confusing
, Jul 7, 2020 >> close it

How to display tools on buttons on model cards.

Show the model config file is accessible, Oct 16, 2020 >> close it

Have an easy way to download the rdf from the model card

Filtering by tags, behavior weird, Sep 25, 2021 >> close it

This bug with the tags is still happening today (22th Nov, 2023).
@cfusterbarcelo write a new issue because tags are now joined by an OR instead of an AND and that should be changed. Tag @jmetz.

(Weize) Quick demo and updates for the imagej-based model testing interface: https://github.com/bioimage-io/bioimage.io/pull/364

November 6th, 2023
Attendees

Name
affiliation
username (github)

Iván Hidalgo
IGC
@IvanHCenalmor

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Mariana Ferreira
IGC
@mariana-gferreira

Joran Deschamps
HT
@jdeschamps

Mehdi Seifi
HT
@mese79

Vera Galinova
HT
@veegalinova

Jeremy Metz
KTH / Scilifelab
@jmetz

Daniel Franco
DIPC / EHU
@danifranco

Weize Xu
KTH (visting)
@Nanguage

Florian Jug
HT
@fjug

Arrate Muñoz
UC3M
@arratemunoz

Agenda

(Dani) BiaPy Intro (https://biapy.readthedocs.io/en/latest/)

GUI/Colab/Jupyter/Docker/Terminal interface for launching bioimage analysis workflow
Handle varies types of inputs including zarr
input -> preprocessing -> train/inference -> postprocessing
support chunks and multi-gpu
Use a config file (yaml) to create the workflow
WIP: CI for BMZ
All crop/merge functions: https://github.com/danifranco/BiaPy/blob/master/data/data_3D_manipulation.py . To pass an image through the model and generate the prediction with padding and overlap we mainly do two steps:

Extract Zarr patch taking into account padding/overlap: https://github.com/danifranco/BiaPy/blob/3deaeb10c4c72431e580e42dd74cec796f9f5d9c/data/data_3D_manipulation.py#L686
Insert patch into its position in a Zarr/H5: https://github.com/danifranco/BiaPy/blob/master/engine/base_workflow.py#L1538C9-L1538C9

(Joran) Started a discussion on OME-NGFF specs and AI4Life, please have a look and give us your thoughts: https://github.com/bioimage-io/spec-bioimage-io/discussions/543

(Florian) If anyone is interested, I could quickly report on what I learned the BIOCONDA people do with BIOCONTAINERS (one container for each BIOCONDA packate - nuts!)

biocontainers: https://biocontainers-edu.readthedocs.io/en/latest/introduction.html
mulled containers: https://galaxy-lib.readthedocs.io/en/latest/topics/mulled.html
Legal data sharing guru: Oliver Kohlbacher (I'm sure we can ask him one thing every 6 month when we really need to... ;)

BioImage Model Zoo Website, exploring switching to a static site generator(e.g. https://www.pathogens.se/)

(Arrate, Caterina) [New Community Partners] Cell-ACDC (contact: Francesco Padovani from Helmholtz Munich) would like to join the Bioimage Model Zoo as a Community Partner. Should we invite them to attend a Wed meeting? What would be the additional steps for them to become a Community partner?
- (Caterina) will contact them to make them an actual CP, cc Fynn so he can help with the CI once he is back from holidays.

December 6th 2023
Attendees

Name
affiliation
username (github)

Wei Ouyang
KTH
@oeway

Iván Hidalgo
IGC
@IvanHCenalmor

Anna Kreshuk
EMBL
@akreshuk

Mariana Ferreira
IGC
@mariana-gferreira

Joran Deschamps
HT
@jdeschamps

Mehdi Seifi
HT
@mese79

Vera Galinova
HT
@veegalinova

Jeremy Metz
KTH / Scilifelab
@jmetz

Daniel Franco
DIPC / EHU
@danifranco

Weize Xu
KTH (visting)
@Nanguage

Florian Jug
HT
@fjug

Estibaliz Gómez
IGC
@esgomezm

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Agenda

CI for the uploading discussion (Fynn & Jeremy)

Question: does the model work and does the model work for a particular software
Display imjoy icon for all the BioEngine https://github.com/bioimage-io/bioengine-model-runner/blob/gh-pages/manifest.bioengine.yaml

Piximi (Nodar) might interested in working with us on the docker solution for the bioengine
Enable CI for deepimagej (it was disabled to not )
New community partner: BiaPy
Dog Food Hackathon at EMBL (11th-15th March, 2024)
Updates on new test run feature using imagej.js

Using imagej.js to load images with more file format support
Support "arbitrary" image shape through padding and tiling

Format for the next meetings - Proposal

Open rolling notes, GDrive
Linked from the GitHub issue
Establish a system to rotate through partners
Structure: 10-15 mins presentation, rest is discussion around proposed topics
When do we implement it? January 2024

December 13th 2023
Attendees

Name
affiliation
username (github)

Iván Hidalgo
IGC
@IvanHCenalmor

Mariana Ferreira
IGC
@mariana-gferreira

Estibaliz Gómez
IGC
@esgomezm

Carlos García
Pasteur
@carlosuc3m

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Agenda

Advanced postprocessing:

Curtis wanted to develop a cross operator so python and java become compatible and then, we would not neet to reimplement post and preprocessings in java as well.

Abhishek Bhardwaj joined the meeting representing empanada model (Panoptic DeepLab + some important bells and whistles)

They have an entire pytorch_state_dict with the complex postprocessing already included. They have also a ready to upload zip file that will be shared by email to check it. In the long term, they'll try working on torchscript for full cross-compatibility

(Esti, not super important still claimed by users) Access to data programmatically: if this is in the roadmap as a future development, it would be interesting to add a download api in the model card as well. (PD: at the moment, the link in the download buttom of all the datasets points to the official distribution site and is good in all cases.)

More for the future (to discuss with Fynn and add this lines in the roadmap)

(Esti) Pre/post-processing: how easy or difficult is it to contribute to it without being the main developer? Is it modular? A fast/quick mechanism to add those (also in the specs), may be interesting for:

(without assuming that the list of pre/post-processing is going to be static) Easily integrationin both python and java, preserving some synchronisation and easy testing.
Supporting new commers to keep updating the library in an easier way.
New community partners who already have their "definition" and requirements of pre/post-processing. The easy integration of such requirements would facilitate specs adoption and integration of the bioimageio.core library. This would also speed up the cross-compatibility.
It's true that they should be basic processings to keep everything simple but some make sense to integrate (like downsampling images or extremely popular models such as cellprofiler and stardist).

Fynn presenting a roadmap for pre and post-processing status in January/february

Tomaz: if the spec is well structured and documented, it should not be an issue to reimplement these steps.
Esti: somehow for sustainability, someone should be developing it or making this real.

(Esti) When opening an issue in the model card, the author/maintainer of the model does not receive any email, so it's hardly difficult to automatically aware it about any potential problem with the model. Example here: https://github.com/bioimage-io/collection-bioimage-io/issues/652#issuecomment-1759656997

Our own log in system for the model upload and bioengine, and also for the interaction with the user/maintainer.
Jeremy: there is already a log in working. This one is for uploading models and in the future, use the server, gpus or any other computational resources.
In this system, the conversations and issues about each model will be stored as json file. Then a search system could be developed.

December 20th 2023
Attendees

Name
affiliation
username (github)

Iván Hidalgo
IGC
@IvanHCenalmor

Mariana Ferreira
IGC
@mariana-gferreira

Estibaliz Gómez
IGC
@esgomezm

Carlos García
Pasteur
@carlosuc3m

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Agenda

The upload is still down. When a model is uploaded through zenodo, it is not published in the BioImage Model Zoo.
New meeting structure: keep HackMD format. Add only rotation among partners

Next meeting agenda

(Caterina) Retake it or close it?: Bioimage.io Issues.

Packager sometimes fails to download files, still creates zip #171

Has anyone experienced this? Is this still happening?

Partners component is off-center #177 Related to this PR: Center community partners on view #323

It seems it's too old to be merged and it is already fixed. Which would be the procedure for the PR?

Cover images not shown in model cards #258

Real issue at the end of the conversation. Is this fixed now?

January 17th 2024
Attendees

Name
affiliation
username (github)

Wei Ouyang
KTH
@oeway

Jeremy Metz
KTH / Scilifelab
@jmetz

Anna Kreshuk
EMBL
@akreshuk

Joran Deschamps
HT
@jdeschamps

Mehdi Seifi
HT
@mese79

Vera Galinova
HT
@veegalinova

Iván Hidalgo
IGC
@IvanHCenalmor

Estibaliz Gómez
IGC
@esgomezm

Arrate Muñoz
UC3M
@arratemunoz

Matthew Hartley
EBI
@matthewh-ebi

Agenda

New meeting format

(Joran): Sign up for the wednesday meetings presentations
Volunteers presenting on wednesday, should ensure that there's someone presenting next week.

WP6 update: Presentation (slides)

Anna suggested getting in touch with Globias for the reviewing
Matthew also suggested the Tuesday interest group meeting (organized by Aastha)
Discussed MP from partners on tasks 6.1 and 6.2 (grant agreement)
CellPose in browser would be incredibly useful for the OC (could be potentially logged as MP)
RandomForest tasks (consultation or OC projects) could be kicked towards EMBL-HD
Involve Wei and Anna in the OC discussions and selection of the OC team for this year

Status of the new upload feature
BioEngine triton launcher, support deploying custom cellpose models and training
Test Run on large images: https://github.com/bioimage-io/collection-bioimage-io/issues/484#issuecomment-1893787675

January 24th 2024
Attendees

Name
affiliation
username (github)

Jeremy Metz
KTH / Scilifelab
@jmetz

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Joran Deschamps
HT
@jdeschamps

Mehdi Seifi
HT
@mese79

Iván Hidalgo
IGC
@IvanHCenalmor

Estibaliz Gómez
IGC
@esgomezm

Agenda

Presentation AI4Life WP updates - postponed to next week
Presentation from Oded Rotem about the DISCOVER model

Link to paper
They had difficulties understanding what needs to go in the RDF file

Uploaded&accepted models not shown in the zoo (Fynn and Esti take care of this)
(Joran): we are planning a full day of model upload (Jug lab + Open Calls). Who would be willing to be on a hotline support? We would fix a date

Jeremy will let them know once the new upload system is in a state to be tested
Then they will fix a date together
Great time to potentially try the new specs!

February 7th 2024
Attendees

Name
affiliation
username (github)

Mariana Ferreira
IGC
@mariana-gferreira

Jeremy Metz
KTH / Scilifelab
@jmetz

Mehdi Seifi
HT
@mese79

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Anna Kreshuk
EMBL
@akreshuk

Arrate Muñoz
UC3M
@arratemunoz

Vera Galimova
HT
??

Tomaz Vieira
EMBL
??

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Wei Ouyang
KTH
@oeway

Agenda

Tomaz Vieira: local model builder

fully local model builder
not write yamls by hand for many good reasons
discussion with Jeremy about web compatibility
hopefully consolidation can be reached for v0.5

Validator in Rust? with potential wrappers in Python, JS and Java?

Validation of generative models

Fix the seed to a value, e.g. 0 is proposed
https://github.com/bioimage-io/collection-bioimage-io/pull/705#issuecomment-1916139893
https://github.com/bioimage-io/collection-bioimage-io/pull/686

(Caterina) Retake it or close it?: Bioimage.io Issues.

Packager sometimes fails to download files, still creates zip #171

The client on the website might need to be checked. Dominik will be pinged to confirm if the issue persists. Wei needs a model to reproduce.

Partners component is off-center #177 Related to this PR: Center community partners on view #323

It seems it's too old to be merged and it is already fixed. Which would be the procedure for the PR?

Cover images not shown in model cards #258

Real issue at the end of the conversation. Is this fixed now?

February 14th 2024
Attendees

Name
affiliation
username (github)

Mariana Ferreira
IGC
@mariana-gferreira

Iván Hidalgo
IGC
@IvanHCenalmor

Jeremy Metz
KTH / Scilifelab
@jmetz

Mehdi Seifi
HT
@mese79

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Anna Kreshuk
EMBL
@akreshuk

Arrate Muñoz
UC3M
@arratemunoz

Vera Galimova
HT
??

Tomaz Vieira
EMBL
??

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Weize Xu
KTH(visiting)
@Nanguage

Agenda

Update to the uploader's backend

A email confirmation has been added: the user needs to agree that the email will be added to the rdf file.
Wei has suggested to move the Login from the begging. It might be better to be asked just before the user clicks the 'Submit model' buttom.

BioEngine updates: triton launcher for HPC, containers etc.

https://github.com/aicell-lab/triton-launcher
by Weize

Demo of bioengine-web-client:

Online instance: https://bioimage-io.github.io/bioengine-web-client/
GitHub repo: https://github.com/bioimage-io/bioengine-web-client

New models do not show in the BioImage Model Zoo: https://github.com/bioimage-io/collection-bioimage-io/pull/700

BioImage.IO Meeting Minutes
February 21th 2024
:::info
Time: 4:00PM CET (your timezone)
Where: Zoom Channel
:::
Attendees

Name
affiliation
username (github)

Mariana Ferreira
IGC
@mariana-gferreira

Iván Hidalgo
IGC
@IvanHCenalmor

Mehdi Seifi
HT
@mese79

Vera Galimova
HT
??

Tomaz Vieira
EMBL
??

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Weize Xu
KTH(visiting)
@Nanguage

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Florian Jug
HT
@fjug

Wei Ouyang
KTH
@oeway

Agenda

WP6 Open Challenges, presentation available here. @vera
Uploading all models from Open Call 1 to the BMZ format (in Heidelberg?)
Three projects from the OC to be in the Open Challenges:

Leaf segmentation challenge: Instance Segmentation + tracking for fine-tuning
Organelle Segmentation Challenge: 3D Segmentation of plankton cell (data not recieved yet)
Microscopy Denoising Challenge: 2D and 3D denoising tasks

Grand Challenge Platform

Data will be hosted on zenodo
Submissions in docker containers
Inference in AWS

Starting challenges at the end of March
Document with challenge organization info: here
Containers for testing the solutions and the correct format for the trained models to be in the zoo.

Documentation
Contianerisation methods (hello world container provided by the participant)

Relevant methods, make a list and motivate them to participate and create an updated leaderboard.
Wei: is it possible to ask the people to submit the models to the BioImage Model Zoo format?
Meetings about OC on fridays
Update on the new versoin of core: when? soon.

Also setting up the CI

Quick note on CC-BY(-*)
Hackathon in Heidelberg (March). Should there be a roadmap or agenda? (agenda)

In need for a title and a short abstract: everything we want to do around the model zoo.

Mini-hackathon and/or solvathon on May 6&7 2024.

EMBO Course 8th of May in Milano
Who wants to come?
Hackathon topics: WP6 Challenges and Open Calls or Workflows.

workflow related:

https://github.com/bioimage-io/workflows-bioimage-io-python
AI4Life OC on workflowhub: https://workflowhub.eu/projects/228

February 28th 2024
Attendees

Name
affiliation
username (github)

Wei Ouyang
KTH
@oeway

Mariana Ferreira
IGC
@mariana-gferreira

Iván Hidalgo
IGC
@IvanHCenalmor

Mehdi Seifi
HT
@mese79

Vera Galimova
HT
??

Tomaz Vieira
EMBL
??

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Weize Xu
KTH(visiting)
@Nanguage

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Joran Deschamps
HT
@jdeschamps

Jeremy Metz
KTH
@jmetz

Arrate Munoz-Barrutia
UC3M
@ArrateMunoz

Agenda

WP7 presentation by Bea
BioImage.IO Chatbot updates

Preprint: https://arxiv.org/abs/2310.18351
Github: https://github.com/bioimage-io/bioimageio-chatbot/
Performance improvements, implementing ReAct loop in the retrieval process
Knowledge base integration:

biii.eu bioimage informatics index
image.sc forum
web search via duckduckgo
5~8 bioimage analysis books is adding to the knowledge base.

WIP: Extension mechanism for calling external API which allows:

Running imagej macro
Run models (+cellpose) via BioEngine
Run python scripts

OpenAI GPTs:
Test it here:

Test link (need to signup and approval): https://staging.chat.bioimage.io/assistants

Euro-BioImaging Virtual Pub - this Friday!

March 6th 2024
Attendees

Name
affiliation
username (github)

Wei Ouyang
KTH
@oeway

Mariana Ferreira
IGC
@mariana-gferreira

Iván Hidalgo
IGC
@IvanHCenalmor

Tomaz Vieira
EMBL
@Tomaz-Vieira

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Joran Deschamps
HT
@jdeschamps

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Fynn Beuttenmüller
EMBL
@fynnbe

Constantin Pape
Uni Göttingen
@constantinpape

Weize Xu
KTH(visiting)
@Nanguage

Agenda

WP4 presentation - Containerisation
Hackathon in HD:

CellPose model, what's the issue?

What's the state of runnig the model online? --> It's working, refresh your browser!

https://github.com/bioimage-io/bioimage.io/issues/373 --> Anwsered

BioEngine updates:

Plan for BioEngine Apps https://github.com/bioimage-io/bioengine

What's the status of next spec version? @Fynn
Small Open Calls and Challenges (WP6) hackathon in Milan (6th, 7th May), register
SPECS for workflows/bioengine apps/dl4miceverywhere notebooks: find a way to add conda environments (env.yamls or any other agreed format) into the rdf file so the same conda env can be called from all these software.

March 20th 2024
Attendees

Name
affiliation
username (github)

Wei Ouyang
KTH
@oeway

Mariana Ferreira
IGC
@mariana-gferreira

Iván Hidalgo
IGC
@IvanHCenalmor

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Fynn Beuttenmüller
EMBL
@fynnbe

Joran Deschamps
HT
@jdeschamps

Florian Jug
HT
@fjug.

Tomaz Vieira
EMBL
@Tomaz-Vieira

Weize Xu
KTH(visiting)
@Nanguage

Vera Galinova
HT
??

Agenda

Schedule is empty: here

Anyone who is willing to present something, please add yourself there!

WP3 meeting happening tomorrow at 14:00h

Documentation rework >> first approach
June Hackathon (workshop + hackathon + uploathon)

Something about Heidelberg

Introduction, work groups, outcomes, summary of the Hackathon
Hackathon (partial) outcomes slides: not every work group had slides, refer to the first link for more details

Open Call Reviewers: Review! (new form link!!! see Bea last email)
New announcement channel on Element, post important news there! (e.g. "new documentation is out, please give feedback!")
Taking over maintenance of the uploader:

A dedicated room for this in Element is created
Increase bus factor for uploader maintenance

Move partner test scripts (only this for the moment) in GitHub to:

a) the bioimage-io organization
b) a new organization dedicated to it
c) 🏆 Only one repo in the bioimage-io organization

GTC Updates (Wei) GTC

They do care about life sciences and imaging

Move bioimageio packager to bioimage-io orga (it's in imjoy org now)

move all apps to https://github.com/bioimage-io/bioengine

April 10th 2024
Attendees

Name
affiliation
username (github)

Tomaz Vieira
EMBL
@Tomaz-Vieira

Mariana Ferreira
IGC
@mariana-gferreira

Mehdi Seifi
HT
@mese79

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Fynn Beuttenmüller
EMBL
@fynnbe

Joran Deschamps
HT
@jdeschamps

Arrate Muñoz-Barrutia
UC3M
@arratemunoz

Wei Ouyang
KTH
@oeway

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Agenda

The Chatbot is now working (yes, now it is working not as las time when it was "working"). Test it here: https://bioimage.io/chat/
Google form to express interest (not registration yet!) to come to Madrid in June and give a Talk/Workshop.

Please do it before Friday!
We will send a registration link for the actual hackathon/uploathon soon! ^^
Organization:

10th to the 14th of June in Madrid
2 days workshops and talks (for students)
3 days parallel hackathon and uploathon

BMZ Typeform question: "I am looking to quantify osteons from SEM images. I tested all the models in the zoo and didn't find any that were quite the right fit (of course). I wonder if you might be able to recommend one or provide some advice."

If there is a question on the typeform and there is no model available to segment those images... what do we do?

Should we point them to other software? An email consultancy showing them other things to try.
Potential things:

SAM, SAMJ, microSAM
Looking at the tool used here: https://github.com/ai4life-opencalls/oc_1_project_52, also SAM based

Status of the bioimage.io > are all models displayed?

no, not yet

ok with public list of reviewers? (emails)

we'll use github account ids with a mapping to names in the collection repo

EU-OpenScreen wondering what they should do to fill their PMs in AI4Life, should I put them in touch with WP7?

Yes! Kathy Skopelitou seems to be replacing Katja

Plan for the next deliverable for BioEngine

April 10th 2024
Attendees

Name
affiliation
username (github)

Tomaz Vieira
EMBL
@Tomaz-Vieira

Mariana Ferreira
IGC
@mariana-gferreira

Mehdi Seifi
HT
@mese79

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Fynn Beuttenmüller
EMBL
@fynnbe

Joran Deschamps
HT
@jdeschamps

Arrate Muñoz-Barrutia
UC3M
@arratemunoz

Wei Ouyang
KTH
@oeway

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Agenda

The Chatbot is now working (yes, now it is working not as las time when it was "working").
Google form to express interest (not registration yet!) to come to Madrid in June and give a Talk/Workshop.

Please do it before Friday!
We will send a registration link for the actual hackathon/uploathon soon! ^^
Organization:

10th to the 14th of June in Madrid
2 days workshops and talks (for students)
3 days parallel hackathon and uploathon

BMZ Typeform question: "I am looking to quantify osteons from SEM images. I tested all the models in the zoo and didn't find any that were quite the right fit (of course). I wonder if you might be able to recommend one or provide some advice."

If there is a question on the typeform and there is no model available to segment those images... what do we do?

Should we point them to other software? An email consultancy showing them other things to try.
Potential things:

SAM, SAMJ, microSAM
Looking at the tool used here: https://github.com/ai4life-opencalls/oc_1_project_52, also SAM based

Status of the bioimage.io > are all models displayed?

no, not yet

ok with public list of reviewers? (emails)

we'll use github account ids with a mapping to names in the collection repo

EU-OpenScreen wondering what they should do to fill their PMs in AI4Life, should I put them in touch with WP7?

Yes! Kathy Skopelitou seems to be replacing Katja

Plan for the next deliverable for BioEngine

April 17th 2024
Attendees

Name
affiliation
username (github)

Tomaz Vieira
EMBL
@Tomaz-Vieira

Mariana Ferreira
IGC
@mariana-gferreira

Mehdi Seifi
HT
@mese79

Fynn Beuttenmüller
EMBL
@fynnbe

Joran Deschamps
HT
@jdeschamps

Arrate Muñoz-Barrutia
UC3M
@arratemunoz

Wei Ouyang
KTH
@oeway

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Vera Galinova
HT
??

Agenda

Model uploader, is it done? --> Urgent to plan next week's course

Jeremy is around finishing dev work.
https://github.com/bioimage-io/bioimageio-uploader-service
At the moment the netlify functions that served as a light backend before are being moved into the hypha service. Jeremy is actually doing this at the moment.
A basic uploading back up should be there again in a couple days

Bug in new models appearing in the website, is it solved? (Empanada models are under review)

MicroSAM models from Constantin are uploaded to the connection (Anna said it was smooth) but they are still not displayed in the website

Model retraining --> is there some toy code I could reuse for fine-tuning (out of the specs and bioimageio)

Paper resubmission?

Model upload
CI

bioimageio core is quite stable already so the notebooks can start being migrated

EBI course:

Anna gives the talk and shows the website (1h)

Dominik (1.15h)

Wei (30 mins) and Esti (1h) (after lunch)

Ask Dominik to switch the order (ESTI)

Ask craig to make more GPUs available for the test run to not collapse with Anna and the 40 participants (ESTI)

Bioengine HPC worker

Python package to install it
Then the user will be able to access their institutional HPC from the BioImage Model Zoo website and get new functionalities in the test run button. Basically this would support the use of local HPC from the browser.
It works with Singularity

April 24th 2024
Attendees

Name
affiliation
username (github)

Mariana Ferreira
IGC
@mariana-gferreira

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Ivan Hidalgo
IGC
@IvanHCenalmor

Tomaz Vieira
EMBL
@Tomaz-Vieira

Agenda

Is there a meeting next week? We guess that there isn't.

WP4 meeting on the 2nd of April at 15:00 CEST.

May 8th 2024
Attendees

Name
affiliation
username (github)

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Agenda

Workshop & Hackathon/Uploathon in June in Madrid

Please, register in the form here as soon as possible.
Event webpage: here
Is the upload ready and documented?
Is there a list of models that we want to upload?

May 15th 2024
Attendees

Name
affiliation
username (github)

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Constantin Pape
Uni Goettingen
@constantinpape

Mariana Ferreira
IGC
@mariana-gferreira

Iván Hidalgo
IGC
@IvanHCenalmor

Wei Ouyang
KTH
@oeway

Nils Mechtel
KTH
@nilsmechtel

Fynn Beuttenmüller
EMBL
@fynnbe

Arrate Muñoz-Barrutia
UC3M
@arratemunoz

Agenda

[Caterina] Did you recieve my email as a reminder of this meeting yesterday?

Yes :smile:

I2K Workshops:

Beginner BMZ (users): people who don't know BMZ and wants to learn about it and how to use it + chatbot for beginners - @Anna
Advanced BMZ (developers): people who is interested on how BioEngine and core library works - @Esti
BioImage.IO ChatBot (developers) - @Caterina
DL4MicEverywhere - @Esti

Workshop & Hackathon/Uploathon in June in Madrid

Please, register in the form here as soon as possible.
Event webpage: here

Uploathon:

Who is helping, the trainers
Is the upload ready?
Models to upload.
An idea from Anna: have a cool model such as Stardist, fine tune it in a new dataset, do some kind of competition on the best results, then the best one try to upload it to the BMZ (only uploading the best).

[Constantin] SAM Models in the zoo

Is it legal to rehost them?
Rough info on how to bring them into the zoo format?

[Constantin] Updating the zoo to new collection backend

[Constantin] Convenience functionality for prediction

[Constantin] How do I start a kaibu app (question for Wei, if there's time we can discuss, bringing it up here because its also something we should document at some point)

May 15th 2024
Attendees

Name
affiliation
username (github)

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Constantin Pape
Uni Goettingen
@constantinpape

Mariana Ferreira
IGC
@mariana-gferreira

Iván Hidalgo
IGC
@IvanHCenalmor

Wei Ouyang
KTH
@oeway

Nils Mechtel
KTH
@nilsmechtel

Fynn Beuttenmüller
EMBL
@fynnbe

Arrate Muñoz-Barrutia
UC3M
@arratemunoz

Agenda

[Caterina] Did you recieve my email as a reminder of this meeting yesterday?

Yes :smile:

I2K Workshops:

Beginner BMZ (users): people who don't know BMZ and wants to learn about it and how to use it + chatbot for beginners - @Anna
Advanced BMZ (developers): people who is interested on how BioEngine and core library works - @Esti
BioImage.IO ChatBot (developers) - @Caterina
DL4MicEverywhere - @Esti

Workshop & Hackathon/Uploathon in June in Madrid

Please, register in the form here as soon as possible.
Event webpage: here

Uploathon:

Who is helping, the trainers
Is the upload ready?
Models to upload.
An idea from Anna: have a cool model such as Stardist, fine tune it in a new dataset, do some kind of competition on the best results, then the best one try to upload it to the BMZ (only uploading the best).

[Constantin] SAM Models in the zoo

Is it legal to rehost them?
Rough info on how to bring them into the zoo format?

[Constantin] Updating the zoo to new collection backend

[Constantin] Convenience functionality for prediction

[Constantin] How do I start a kaibu app (question for Wei, if there's time we can discuss, bringing it up here because its also something we should document at some point)

May 22th 2024
Attendees

Name
affiliation
username (github)

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Mariana Ferreira
IGC
@mariana-gferreira

Iván Hidalgo
IGC
@IvanHCenalmor

Wei Ouyang
KTH
@oeway

Nils Mechtel
KTH
@nilsmechtel

Fynn Beuttenmüller
EMBL
@fynnbe

Mehdi Seifi
HT
@mese79

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Agenda

Help needed for the last consultation calls
Uploathon in Madrid (12th-14th June)

List of models - draft here

A CellPose model might be uploaded
I encourage all of you to edit and participate in this document to have a full list of models that might be interesting to upload doing the uploathon or in long-term.

Tomaz is doing a GUI to build the models there to get a zip and upload it in to the zoo. That's going to be very useful for the uploathon.
We (BMZ team) need to do a lot of testing on the upload process before the uploathon.

Last Call for Registering to the Hackathon in Madrid! Please, register here. We close the register this friday!

If someone of your group only wants to register for attending the workshop, register here.

Add to documentation rework spec documentation from here.

May 29th 2024
Attendees

Name
affiliation
username (github)

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Mariana Ferreira
IGC
@mariana-gferreira

Iván Hidalgo
IGC
@IvanHCenalmor

Wei Ouyang
KTH
@oeway

Nils Mechtel
KTH
@nilsmechtel

Fynn Beuttenmüller
EMBL
@fynnbe

Mehdi Seifi
HT
@mese79

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Anna Kreshuk
EMBL
@akreshuk

Joran Deschamps
HT
@jdeschamps

Craig Russell
EMBL-EBI
@ctr26

Agenda

Internal Validation Workflow here

Motivation: recommendation to implement an internal way to release the small projects/components that we develop so we can all agree that the material is ready to go and report back.
It is important for internal testing! You can suggest reviewers if you want to point someone to test it.
People is encouraged to add their projects to the workflow. They can be added through issues and PR.
Who is a user of this board? People developing and releasing things and people interested in seeing the status of these small projects or components.

NEW DOCS! Visit them bioimage.io/docs!

Phase two: curate all the available documentation, add missing documentation and generally improve all the content.
Asking your contribution to update all the docs and add the missing documentation. Please give it a look!

Spec Docs (plan for improving the readability of the new version)

Readable version here - outdated
Also here - updated and generated automatically
And here - updated and generated automatically
Ideally: we should have an updated and automatically generated documentation human readable.

EBI S3 storage issue, download extremely slow: https://forum.image.sc/t/micro-sam-issues-in-napari-http/96750/9?u=oeway

Uploathon

Doc here
Any suggestion is encouraged!

Euro-BioImaging Annual report - updated factsheet

June 5th 2024
Attendees

Name
affiliation
username (github)

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Mariana Ferreira
IGC
@mariana-gferreira

Nils Mechtel
KTH
@nilsmechtel

Fynn Beuttenmüller
EMBL
@fynnbe

Mehdi Seifi
HT
@mese79

Vera Galinova
HT
??

Agenda

Issues with the bioimage.io webpage

When clicking to a model and willing to access the source rdf file an error occours:
Sometimes the webpage gets blocked while going from one card to another (don't know how to reproduce or when it happens exactly)

Uploader status
Models to upload.

From the OC.

Two Cellpose retrained models. Looking this notebook to see how they can be exported and uploaded to the zoo.
Some other models from students.

CellPose models.

Missing the post-processing.

PlantSeg.

It's on the way.

Uploathon two options:

Adapt ZeroCostDL4Mic notebook to the new specs - Mariana
Use BiaPy notebooks adapted to the new specs - Dani Franco

WP4 meeting tomorrow 6th June at 15:00h CET
Lisbon hackathon sign up

June 19th 2024
Attendees

Name
affiliation
username (github)

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Mariana Ferreira
IGC
@mariana-gferreira

Mehdi Seifi
HT
@mese79

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Florian Jug
HT
@fjug

Joran Deschamps
HT
@jdeschamps

Iván Hidalgo
IGC
@IvanHCenalmor

Craig Russell
EBI
@ctr26

Anna
EMBL
@akreshuk

Wei Ouyang
KTH
@oeway

Agenda
Madrid Workshop&Uploathon&Hackathon

GitHub Repo with training materials here
All workshop slides have been uploaded to Zenodo AI4Life Community (special thanks to Bea)
Hackathon Recap Slides here

New upload and review method for models.

Maybe we need some documentation on this on how to review models.
More reviewers are needed indeed!
Future work: included models which have not been reviewed with a warning or similar. A link to the model is needed before it is even reviewed and accepted.
Once static and automatic validation has passed, give a link without the need of a reviewer approving the model but under a warning.

Uploathon Recap Slides here

A lot of testing of BiaPy notebooks for re-training BMZ models
A lot of testing on their own data
A lot of future work on training with their own data
One model packaged waited for validation to be uploaded

Model Name
Category
Description
Status
Exported
Uploaded
Notes

µSplit: image decomposition for fluorescence microscopy
Participant Models
Microscopic image splitting
Done
Yes
Yes

DeepContrast
Participant Models
Deep Tissue Contrast Enhancement using Synthetic Data Degradations and OOD Model Predictions
Done
Yes
Yes

OpenCall Cellpose Model 1
Participant Models
Murine Skeletal Muscle Cell Segmentation
Not Started
No
No
Waiting for Qin's cellpose wrapper code

OpenCall Cellpose Model 2
Participant Models
Segmentation of Epithelial Cells
Not Started
No
No
Waiting for Qin's cellpose wrapper code

CellPose Models
Community Interest Models
Pre-trained Cellpose models popular in the community
Not Started
No
No

MobileSAM Encoder
Community Interest Models
Only encoder part of the MobileSAM for feature extraction
Done
Yes
Yes

BMZ Paper Updates

CI for all CP

biapy: Daniel Franco will work on the CI for biapy consumption. He's working on it and already communicating with Fynn. Shouldn't be difficult.
deepImageJ&deepIcy: Carlos will put some time on developping the CI for JDDL that will serve as a CI for both.
Pending:

Test the CI
Document how to do the CI for each CP
Reach to other CP that do not have a CI

Model cards:

Logos, if the logo is not there then is not cross-compatible (Fynn? or who could work on this?)
The CI depends on the collection, which generates the information about which model is compatible with what CP software.
From the CI it should be possible to generate the "links" in the specs that asign the icons in the model card. These icons link to the different apps defined in the zoo.
The icons should be there only when opening the model card.

Documentation for the specs:

Esti, Fynn and Tomaz are working on automatically generating a json file from the Pydantic library (https://github.com/bioimage-io/spec-bioimage-io/pull/614#issuecomment-2172956580).
Current discussion: Parsing the json schema or integratig all the info in

OC

Final recommendations needed this week!

June 26th 2024
Attendees

Name
Affiliation
Username (GitHub)

Mehdi Seifi
HT
@mese79

Vera Galinova
HT
??

Iván Hidalgo
IGC
@IvanHCenalmor

Mariana Ferreira
IGC
@mariana-gferreira

Anna
EMBL
@akreshuk

Wei Ouyang
KTH
@oeway

Nils Mechtel
KTH
@nilsmechtel

Craig Russell
EBI
@ctr26

Agenda

Fine-tuning notebooks by Mariana! (<3)

Fine-tuning models: which models can be fine-tuned and which ones are not? Can we know it and maybe even display it in the model card?
During Madrid's hackathon:

Mariana updated the pytorch notebook for BMZ models with the new core library.
Maraina is updating the notebook that Estibaliz created for the course.

Not all the models can be finetuned, depends in many aspects. For example, the format of the weights, the state of the optimizer or the pre-processing or post-processing.
It would be great to add a tag to indicate if a model is tunable (finetune can be applyed on a notebook or Ilastik).

The test run feature of all the models is tested in here

Models that are not working or not available for testing
frank-water-buffalo	Not available for testing
lucky-fox	Not available for testing
pioneering-goat	Not available for testing
stupendous-sheep	Not available for testing
non-judgemental-eagle	Not Working
creative-panda	Not Working
impartial-shark	Not available for testing
placid-llama	Not Working
naked-microbe	Not Working
easy-going-sauropod	Not Working
efficient-chipmunk	Not available for testing
amiable-crocodile	Not available for testing
diplomatic-bug	Not available for testing
greedy-whale	Not available for testing
noisy-ox	Not available for testing
humorous-crab	Not available for testing
faithful-chicken	Not available for testing
idealistic-rat	Not available for testing
committed-turkey	Not available for testing
decisive-panda	Not available for testing
ambitious-sloth	Not Working
determined-hedgehog	Not available for testing
nice-peacock	Not available for testing

KPIs

Make your suggestions here: https://docs.google.com/document/d/1Htr_u7n-LGszWV7ZLtTPVBOyjfycX1vcB4LtKP4vZwA/edit#heading=h.dvd2qt5kji7e

Distribute and promote the denoising challenge: more applications are needed! -> https://ai4life-mdc24.grand-challenge.org/

July 3rd 2024

Name
Affiliation
Username (GitHub)

Wei Ouyang
KTH
@oeway

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Mariana Ferreira
IGC
@mariana-gferreira

Fynn
EMBL
@FynnBe

Agenda

Which is the state of showing which models can be fine-tuned?

Esti proposes that is something that should not be in the model card
Is more a property of the notebook or a program
Any model except torchscript models can be loaded in code and fine-tuned
It depends on the software that consumes the model, if they offer this capability or not

Login System of bioimage.io is offline (Hypha is down)

some maintainance is being done

Action items:

Upgrade core library in BioEngine

Wei and Fynn having a meeting to solve this.

Go through the failing models from the test run feature and fix as many as possible, remove the rest. Do it after updating the core library in BioEngine.

Documentation:

There is a link here which is wrong > fixed on a PR
README.md

Take the recommendeations on how to write the doc.md for the model outside.
Make a template or save the old one.
Wei and Caterina will do this.
Example of README.md structure: https://bioimage.io/#/?tags=unet&id=10.5281%2Fzenodo.6406756
spec comment on the documentation field

Reviewing process:

Review process described in bioimage-io/collection#76

should this be added to the documentation and made public for people (volunteers to join)?
Esti proposes to be closed for now.

How to assign reviewers to resource drafts?
Do we want set targets for response times along the review process?
Should we have a draft version of the model? How?
@Fynn issue related to CI status: https://bioimageio-uploader.netlify.app/#/status
There's a reviewers channel in Element
The status of each pending model could be updated to "in review" whenever someone decides to (self)assign to it. This needs to be updated

starting point to implement this part in the backend (bioimageio_collection_backoffice) could be here.

AI4EOSC technical team meeting - July 17, will people be available?

July 17th 2024
Attendees

Name
Affiliation
Username (GitHub)

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Mariana Ferreira
IGC
@mariana-gferreira

Iván Hidalgo
IGC
@IvanHCenalmor

Fynn
EMBL
@FynnBe

Nils Mechtel
KTH
@nilsmechtel

Agenda

AI4EOSC presentation and discussion

BioImage Archive integration with AI4EOSC Platform. It is currently integrated with Zenodo. (datahugger could be an option for this integration).

Craig will see if this is possible and how.

BioImage Model Zoo for inference.

Allowing people to deploy the BMZ models in the AI4EOSC platform.
Build a template that every bioimage.io model could be runned on it.
Now models are runned in model containers for AI4EOSC. It could be adapted for our models. It would be a matter of creating a module with the tryton server docker image. Doing the interface with the AI4EOSC API.
Connect it to the notebooks for inference.

BioImage Model Zoo for fine-tuning.

This is something that we can work in the future.

[Caterina] There is a WP3 Meeting tomorrow at 14:00h. You can check the agenda here.

July 24th 2024
Attendees

Name
Affiliation
Username (GitHub)

Wei Ouyang
KTH
@oeway

Nils Mechtel
KTH
@nilsmechtel

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Arrate Muñoz-Barrutia
UC3M
@arratemunoz

Anna
EMBL
@akreshuk

Tomaz Vieira
EMBL
@Tomaz-Vieira

Fynn
EMBL
@FynnBe

Mariana Ferreira
IGC
@mariana-gferreira

Iván Hidalgo
IGC
@IvanHCenalmor

Vera Galinova
HT
@veegalinova

Agenda

Add the notebook that Mariana created, somewhere on the user's documentation to make it more accesible.

How to use the core library(add it here): https://github.com/bioimage-io/core-bioimage-io-python/blob/main/example/model_usage.ipynb

We need to have a the minimal example with just '3 lines of code' with the simplest usecase.

We need to have an image, graph or entry on the documentation that shows how the different repositories inside GitHub's bioimage community are connected in the wiki: https://github.com/bioimage-io/bioimage.io/wiki (Caterina has said that she will try to take care of this)

[Esti] StarDist export does not work with the new bioimageio.core and with the old one, there's no way to run the test-model https://github.com/stardist/stardist/issues/276

[Esti] Model upload not working, at least for models with format 0.4.9 https://github.com/bioimage-io/bioimage.io/issues/415

The problem is not with the uploader itself, but as the specs are more restrictive in the newer version, the new specs are the ones giving the issues.
The fact that the specs are more restrictive is not a good approach.
As far as understood, this problem is only concerning the source field. The source field dissapeared on version 0.3, which happened 3 years ago. Is it worth it to make it recontrabatible to that old versions? Maybe is something to take a look.

The BMZ exportation on ZeroCost notebooks is not working because that part of the notebook is still in the old version. So if someone is retraining a model using a ZeroCost notebook, it will not be able to be updated. This needs to be updated.

[Caterina] Made an updated version of the Feedback form for the BioImage Model Zoo and community parthers here. Please share it! We already have 4 answers!

how to run a model with python

https://github.com/bioimage-io/core-bioimage-io-python/blob/main/example/model_usage.ipynb

[Carlos] Working on the CI for the JDLL almost done. He will have it very soon!

[Caterina] All links from bioimage.io/docs are corrected and working!

[Caterina] WP3 Deliverable, waiting to be commented here

[Caterina] Internal documentation here: https://github.com/bioimage-io/bioimage.io/wiki

[Fynn] onnxruntime seems to have changed such that onnx networks cannot accept input tensors with arbitrary dimensions. (affable-shark is now failing the test)

 index: 2 Got: 64 Expected: 256
 index: 3 Got: 64 Expected: 256
 Please fix either the inputs/outputs or the model.

July 31st 2024
Attendees

Name
Affiliation
Username (GitHub)

Nils Mechtel
KTH
@nilsmechtel

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Arrate Muñoz-Barrutia
UC3M
@arratemunoz

Tomaz Vieira
EMBL
@Tomaz-Vieira

Iván Hidalgo
IGC
@IvanHCenalmor

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Mehdi Seifi
HT
@mese79

Agenda

No meetings in August! Next meeting: 4th of September
The uploader is not accepting models from the previous versions of the specs.
Reminder: WP4 regular meeting tomorrow at 15:00 CEST.

September 18th 2024
Attendees

Name
Affiliation
Username (GitHub)

Tomaz Vieira
EMBL
@Tomaz-Vieira

Anna
EMBL
@akreshuk

Mariana Ferreira
IGC
@mariana-gferreira

Iván Hidalgo
IGC
@IvanHCenalmor

Mehdi Seifi
HT
@mese79

Vera Galinova
HT
@veegalinova

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Agenda

Discuss Demos for the AI4Life general assembly
Demo 1: How can our users create and upload models today? (20’+40’)
(Fynn Beuttenmueller, Mehdi, Tomaz)
Note: all OC and lab specific models need to be added by the GA!!!
Demo 2: How can users consume uploaded models? (20’+40’)
(i) from bioimage.io (Wei Ouyang)
(ii) from community partner tools
(Anna Kreshuk (ilastik); Arrate Muñoz Barrutia, Ignacio Arganda-Carreras (BiaPy))
(iii) from code, notebooks, containers
(Estibaliz Gómez de Mariscal, Ricardo Henriques, Mariana Ferreira)
Demo 3: FAIR is not just a buzzword! (20’+40’)
(i) FAIR and AI-ready datasets (and formats!)
(Matthew Hartley, Teresa Zulueta-Coarasa)
(ii) FAIR AI models via the BioImage Model Zoo (Florian Jug (HT on premise BMZ???))
Note: all OC and lab specific models need to be added by the GA!!!
(iii) FAIR documentation and Chatbot (Arrate Muñoz Barrutia, Caterina 🌴)

We volunteered Mehdi to do model uploads at any level of manual hacking and along the way produce a documentation what steps a full model upload takes, which ones work, which ones are currently creating problems, and who created the existing solution and can help us fix issues and revamp the entire upload process. Thanks Mehdi! #hero

Long discussion in the dev-steering channel about compatibility with Huggingface, why (not) using GH repositories for models, run on community partner tools what it is run in the CI

From Mehdi to FILL please: As we discussed during the yesterday meeting, I am sharing with you a link to the document that we can share our experience / issues / ideas about the uploader and the whole uploading proccess: https://docs.google.com/document/d/1zTTlvGGjoMggYoQ5EMBM7P3fmA4sPBYwL-OurFCl39c/edit?usp=sharing

Wei: Test run on the website

ilastik (Anna): They will run some models there. They need to change to the new version of the spec.

Biapy: CI works. Currently, latest updates and changes related with the manuscript rebuttal. So, Daniel F. and Ignacio A. are checking that everything runs smoothly. Documentation updated. New video tutorials.

ZeroCost (Esti + Mariana + Iván): Work on the update of the notebooks for segmentation to use the new library and specs. This model should be compatible with Ilastik.

Containers (Esti + Mariana + Iván): Container standard specs + bioimageio notebook for loading a model from the zoo and retrain it with publicly available data and export back.

September 25th 2024
Attendees

Name
Affiliation
Username (GitHub)

Tomaz Vieira
EMBL
@Tomaz-Vieira

Anna
EMBL
@akreshuk

Mariana Ferreira
IGC
@mariana-gferreira

Iván Hidalgo
IGC
@IvanHCenalmor

Florian Jug
HT
@fjug

Mehdi Seifi
HT
@mese79

Vera Galinova
HT
@veegalinova

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Teresa Zulueta-Coarasa
EBI
@tzulueta

Agenda

Update on current state of the art of model uploading

Mehdi (and Tomaz (and others)) prepare a comprehensive document that describes how the current uploader + CI + model storage + model serving + model testing workflow is set up. Each part should be mentioned, currently problems and hardware on which it runs, plus know isses should be listed. Additionally it would be nict to know who created the current modules so we know who we can ask if questions or issues arise.
CellPose model was uploaded to zoo by Mehdi

The download button of the bioimage.io website is not working for some time now.

We need to have someone else a part from Wei being able to manage this and having the keys to the castle.

Demos schedule:

Septmber 25th - first trial runs of demos
October 2nd - second trial run of demos (not Jug Lab, sorry, we are all at ECCV)
October 9th - full demo run of all involved

Demos:
Demo 1: How can our users create and upload models today? (20’+40’) (Fynn Beuttenmueller, Mehdi, Tomaz > create/GUI tool)
Note: all OC and lab specific models need to be added by the GA!!!
Demo 2: How can users consume uploaded models? (20’+40’)

(i) from bioimage.io (Wei Ouyang)
(ii) from community partner tools (Anna Kreshuk (ilastik); Arrate Muñoz Barrutia, Ignacio Arganda-Carreras (BiaPy))
(iii) from code, notebooks, containers (Estibaliz Gómez de Mariscal, Ricardo Henriques, Mariana Ferreira)

Demo 3: FAIR is not just a buzzword! (20’+40’)

(i) FAIR and AI-ready datasets (and formats!) (Matthew Hartley, Teresa Zulueta-Coarasa)
(ii) FAIR AI models via the BioImage Model Zoo (Florian Jug (HT on premise BMZ???))
Note: all OC and lab specific models need to be added by the GA!!!
(iii) FAIR documentation and Chatbot (Arrate Muñoz Barrutia, Caterina 🌴)

PREPARE SOMETHING FOR NEXT WEEK!

Chatbot talk on Friday at 14pm for GloBIAS. More info here: GloBIAS Seminar Series

October 2nd 2024
Attendees

Name
Affiliation
Username (GitHub)

Tomaz Vieira
EMBL
@Tomaz-Vieira

Anna
EMBL
@akreshuk

Iván Hidalgo
IGC
@IvanHCenalmor

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Agenda

GA Demos:
Demo 1: How can our users create and upload models today? (20’+40’) (Fynn Beuttenmueller, Mehdi, Tomaz > create/GUI tool)
Note: all OC and lab specific models need to be added by the GA!!!
Demo 2: How can users consume uploaded models? (20’+40’)

(i) from bioimage.io (Wei Ouyang)
(ii) from community partner tools (Anna Kreshuk (ilastik); Arrate Muñoz Barrutia, Ignacio Arganda-Carreras (BiaPy))
(iii) from code, notebooks, containers (Estibaliz Gómez de Mariscal, Ricardo Henriques, Mariana Ferreira)

Demo 3: FAIR is not just a buzzword! (20’+40’)

(i) FAIR and AI-ready datasets (and formats!) (Matthew Hartley, Teresa Zulueta-Coarasa)
(ii) FAIR AI models via the BioImage Model Zoo (Florian Jug (HT on premise BMZ???))
Note: all OC and lab specific models need to be added by the GA!!!
(iii) FAIR documentation and Chatbot (Arrate Muñoz Barrutia, Caterina)

(Iván) Issues on some of the uploaded models:

🐸 gleeful-bird and 🐸 poisonous-raccoon have a different animal emoji.
There is a model called: 🐙 10.5281/zenodo.8421755
🦥 ambitious-sloth is not accesible.

(Iván) Questions for reviewing process:

Where can I find the actual model or the rdf of the uploaded models?
What does the feedback in the uploaded models mean? Because there are CI outputs with a cross and the CI has passed correctly.
Where can I now what I have to change to finally accept the model?

(Iván) Tomorrow, 3rd of October at 15:00 CEST, it will be WP4 regular meeting.

(Carlos) Cannot attend today, but will try to have deepImageJ and DeepIcy demos for next week. Integration of BiaPy in Java based software.

(Tomaz) Which are the differences between the Uploader and the GUI? The GUI is more like a complete solution and you can also run it locally and even test the model if you have core installed. It's another way to access the same thing.

(Tomaz) The new dev-docs, with flatened classes and examples, is here: https://github.com/bioimage-io/spec-bioimage-io/pull/630 . I see now that our CI is broken again because pyight updated is now producing other type checking errors, but you can use the PR anyway.

(Caterina) I2K BioImage Model Zoo workshops.

Share the feedback form after it: https://forms.gle/c2KUxyAa3zMj2Hz57

October 16th 2024
Attendees

Name
Affiliation
Username (GitHub)

Tomaz Vieira
EMBL
@Tomaz-Vieira

Anna
EMBL
@akreshuk

Iván Hidalgo
IGC
@IvanHCenalmor

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Arrate Muñoz-Barrutia
UC3M
@arratemunoz

Carlos
UC3M
@carlosuc3m

Vera Galinova
HT
@veegalinova

Florian Jug
HT
@fjug

Mehdi Seifi
HT
@mese79

Marcus Andersson
KTH
@marcus1337

Ricardo Henriques
IGC/GIMM/ITQB
@henriqueslab

Mariana Ferreira
IGC
@mariana-gferreira

Nils Mechtel
KTH
@nilsmechtel

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Ignacio Arganda-Carreras
UPV/EHU
@iarganda

Teresa Zulueta-Coarasa
EBI
@tzulueta

Fynn
EMBL
@FynnBe

Daniel Franco-Barranco
EHU/UPV & DIPC
@danifranco

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Wei Ouyang
KTH
@oeway

Agenda

GA Demos:
Demo 1: How can our users create and upload models today? (20’+40’) (Fynn Beuttenmueller, Mehdi, Tomaz > create/GUI tool)
Note: all OC and lab specific models need to be added by the GA!!!
Demo 2: How can users consume uploaded models? (20’+40’)

(i) from bioimage.io (Wei Ouyang) >> decide what model to show and who presents this, preferably, not affable-shark
(ii) from community partner tools (Anna Kreshuk (ilastik); Arrate Muñoz Barrutia, Ignacio Arganda-Carreras (BiaPy); Carlos and the new deep(not)ImageJ demo...)
(iii) from code, notebooks, containers (Estibaliz Gómez de Mariscal, Ricardo Henriques)

Demo 3: FAIR is not just a buzzword! (20’+40’)

(i) FAIR and AI-ready datasets (and formats!) (Matthew Hartley, Teresa Zulueta-Coarasa)
(ii) FAIR AI models via the BioImage Model Zoo (Florian Jug (HT on premise BMZ???))
Note: all OC and lab specific models need to be added by the GA!!!
(iii) FAIR documentation and Chatbot (Arrate Muñoz Barrutia, Caterina)

October 30th 2024
Attendees

Name
Affiliation
Username (GitHub)

Tomaz Vieira
EMBL
@Tomaz-Vieira

Anna
EMBL
@akreshuk

Iván Hidalgo
IGC
@IvanHCenalmor

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Arrate Muñoz-Barrutia
UC3M
@arratemunoz

Vera Galinova
HT
@veegalinova

Marcus Andersson
KTH
@marcus1337

Mariana Ferreira
IGC
@mariana-gferreira

Nils Mechtel
KTH
@nilsmechtel

Fynn
EMBL
@FynnBe

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Wei Ouyang
KTH
@oeway

Joran Deschamps
HT
@jdeschamps

Agenda

(Caterina) Is any of you experiencing issues to download models from the BioImage.IO? Image.sc Forum question

Maybe it's related to this issue
There seems to be an error when downloading a model with the ilastik button, Wei will look into that

(Mehdi, Vera and Caterina) Problems and suggestions with the reviewing process:

Current reviewing process is mostly limited to mounting the S3 bucket and browse for models!
One credential for everyone in S3 bucket with rights to everything... a bit dangerous
Reading error logs on uploader to find out what went wrong can be a bit tricky
Do we really need sample input/output and producing exact the same result? (no other zoos has this)

[Wei] It can bring some issues in terms of hardware but it's the only way we can detect the errors that are in between (with the CI). It's the way to give us confidence that the model can be reproduced. "We should keep that"

Having the main contributor of the model stated in the model being reviewed would be helpful
Having a link or access to download the whole model would also be helpful and faster
Seeking assistance: some models have the same error ("reproduce test outputs from test inputs")... which would be the steps to follow on this error?
TO DO: Create an issue about this suggestions such as adding the contributor name or the link to the model, add a conda environment that can be used to test the model (uploader repo)

(Iván) Uploader is randomly failing: Video where same model fail and success. In case some demo plans to use it, to be aware.

We need the error log to see what's happening. Make an issue!

(Wei) Should we serve uploaded model as it is or we upgrade it? E.g. after new spec release.

When a new format version is released, we should update all the models or should they remain as the user upload them.
Think how much backward compatibility we should provide.
Think reproducibility for published models without dated consumer software.
Who updates the model? What if the people who contributed do not update it? Should only be the user or could another person update the model.
All the versions are published, the user just need to point that version (this could fix consumer's comatibility problems).
There is the parent field that can point to an older model version, but that would overpopulate the zoo with cloned models.
Bring this to a steering committee for a decision.

(Wei) Next steps for the uploader: Artifact Manager

November 5th 2024
Attendees

Name
Affiliation
Username (GitHub)

Anna
EMBL
@akreshuk

Fynn
EMBL
@FynnBe

Iván Hidalgo
IGC
@IvanHCenalmor

Mariana Ferreira
IGC
@mariana-gferreira

Florian Jug
HT
@fjug

Vera Galinova
HT
@veegalinova

Mehdi Seifi
HT
@mese79

Wei Ouyang
KTH
@oeway

Arrate Muñoz
UC3M
@arratemunoz

Agenda

One of the main concerns that has arrise more than once is the difference between testing a model locally and on CI.

A possible proposal is using a conda environment that is the same one used on CI.
This could be in a checklist for the reviewing proces.
Using conda, issues might appear basen on the local architecture, still on those scenarios the user could go to the kubernetees option.
There can be a different default environments for each weight format.

The reviewing needs to have a checklist that facilitates the process.

Common checklist (upload and review) -- Caterina (@cfusterbarcelo): Please, work in the review guidelines. Give the questions below try and see if they are obvious and make or not sense.

Are the authors correct/updated?
Is the name meaningful?
Does the description make sense?
Are the citations relevant and complete?
Are all the checkmarks green? (aka did test_model()'s output have status=passed?)
Is contributed code limited to what is required to exec the model?
Are tags consistent with the description?

Checklist specific to upload
Checklist specific to review
@Fynn: Propose to make a review summary (for example, a small web page report). Automatically generated that contain the answer to the questions.

Any issue with the uploader: create an Issue on the bioimageio GitHub repository: https://github.com/bioimage-io/bioimage.io/issues

There are Licenses like the one of CellPose that are not recognised by Zenodo, but should be included. How is the way to add it to the model description? Medhi (@mese79) will create an issue of it on the bioimageio.spec repository.

To add a parent model, it needs to be previously added to the rdf.yaml as a field: parent: {"id": "affabel-shark/1.1"}.

Reduce hard requirements for ModelDescr

Use 'alert level' to define threshold for sharing/upload to bioimage.io

update recommended env to ensure compatibility to collection backoffice (e.g. py>=3.9)

November 13th 2024
Attendees

Name
Affiliation
Username (GitHub)

Anna
EMBL
@akreshuk

Iván Hidalgo
IGC
@IvanHCenalmor

Mariana Ferreira
IGC
@mariana-gferreira

Florian Jug
HT
@fjug

Vera Galinova
HT
@veegalinova

Mehdi Seifi
HT
@mese79

Wei Ouyang
KTH
@oeway

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Agenda

Draft models

Feeback from reviewing draft models:

Change the author of the model to the contributor of the model. Add this to this issue.
In the documentation, the warnings when building a model should be better documented (eg. validation section, link for the training data, cover, etc.). Here: https://bioimage.io/docs/#/guides/developers-guide?id=models-in-the-bioimage-model-zoo
A template for the README in the model is a good practise:
Example of README.md structure: https://bioimage.io/#/?tags=unet&id=10.5281%2Fzenodo.6406756
The time shown on the uploaded models is not the real one, but the current time. TODO: fix it.
Indicate in the documentation that pytorch version should not have the -cu12 on it. For example, pytorch_version: 2.2.0-cu12 does not work, it should be pytorch_version: 2.2.0.

Add CI tests for existing models in the model zoo for bioimageio.core

November 20th 2024
Attendees

Name
Affiliation
Username (GitHub)

Anna
EMBL
@akreshuk

Iván Hidalgo
IGC
@IvanHCenalmor

Mariana Ferreira
IGC
@mariana-gferreira

Florian Jug
HT
@fjug

Vera Galinova
HT
@veegalinova

Mehdi Seifi
HT
@mese79

Wei Ouyang
KTH
@oeway

Marcus Andersson
KTH
@marcus1337

Estibaliz Gómez de Mariscal
IGC
@esgomezm

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Agenda

[Anna and Florian] Project board and feature releases checks

Specifically asked by the project reviewer.
Somehow either use it or at least fill it post-hoc with some of the activities.

New test model button on the updloader section: To avoid filling the GPU memory, instead of using Docker, Ray can be a good alternative. Ray allows to create environments and run code within those environments. Ray also caches the packages installed using the conda environment.

Artifact manager: Have an API that directly uploads a model to the BioImage Model Zoo. The artifact manager will avoid the need to connect directly to the S3 to modify managing. This will also help to leverage the work that the CI does, separating the CI and the website; avoiding the cases where the website was breaking because of the CI.

November 27th 2024
Attendees

Name
Affiliation
Username (GitHub)

Anna
EMBL
@akreshuk

Iván Hidalgo
IGC
@IvanHCenalmor

Mariana Ferreira
IGC
@mariana-gferreira

Vera Galinova
HT
@veegalinova

Mehdi Seifi
HT
@mese79

Wei Ouyang
KTH
@oeway

Marcus Andersson
KTH
@marcus1337

Arrate Muñoz
UC3M
@arratemunoz

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Agenda

Marcus Andersson is presenting the "Autoscaler" a project that he has been working on:

GitHub repository: https://github.com/aicell-lab/autoscaler
Create a Hypha service to conect with Slurm and Ray.
Slurm by its own has many problems (needs a Linux terminal, many steps, many GPUs)
So by having Ray on top of Slurm, this brings "easy to use", "scalable GPUs", etc. Fixing with this previous issues.
Goal: Implement a more generic test run feature

About the "Output and expected output disagree" error, can we put a more generous tolerance?
example failed model: https://bioimageio-uploader.netlify.app/#/status/famous-fish

THE paper.

Too many things changed in the actual model zoo that the text should be changed accordingly.
Can we display what models can run on what tools?

BiaPy, Ilastik, Ceramics, deepImageJ (about to)

Make sure that the models are there and working. Upload your models!
Some models the testing functionality is not working. The backend doesn't support pytorch state dict. So, in these models it's disabled.
Authors: possible way to handle the order: apart from first four and last four, have them alphabetically. Include people from the CPs. Other options to be discussed by e-mail with all authors of the original preprint, Anna will show a list of potential additions next time.

Issue: the number of models in the collection json and the ones in the website is not the same.

Online hackathon for the bioimage.io.

Get a date in which all the interested parties can save a day to do this and meet online.
Make a list of all the things that needed to be done for this hackathon FOR NEXT WEDNESDAY.
Check the "help wanted" and "good first issue" issues to start contributing to new repos that you might like

Leave issue in collection about this: https://bioimage.io/#/?id=10.5281%2Fzenodo.6338614

December 04th 2024
Attendees

Name
Affiliation
Username (GitHub)

Anna
EMBL
@akreshuk

Iván Hidalgo
IGC
@IvanHCenalmor

Mariana Ferreira
IGC
@mariana-gferreira

Vera Galinova
HT
@veegalinova

Mehdi Seifi
HT
@mese79

Wei Ouyang
KTH
@oeway

Marcus Andersson
KTH
@marcus1337

Arrate Muñoz
UC3M
@arratemunoz

Caterina Fuster-Barceló
UC3M
@cfusterbarcelo

Tomaz
EMBL
@Tomaz-Vieira

Beatriz Serrano-Solano
Euro-BioImaging
@beatrizserrano

Agenda

What if the models appear as "community contribution" without any reviewing process but state it clearly on the model card.

Maybe this is a discussion for the steering committee?
(Fynn) What if we do not review manually at all? Or do an open review post-publish (aka the cummunity comments on the model).
(Fynn) If we do want to drop human review, we should think what/how we can further improve automatic testing, e.g. enforce the documentation to follow a given template? split it up into individual documentation sections via spec?
(Mehdi) He is in favour that if the model pass the test, it should be accepted.
(Caterina) What about misuse of the models such as in covers and others?
(Mehdi) We shouldn't put efforts on this small cases.
It is important that the person who uploads the model is responsible for what have been uploaded.
(Mehdi) Having a like or dislike button for the model. Or maybe stars, some way to rank it.
(Caterina) The problem with the rankings could be that someone uses the model for something what it's not expected to be and ranks it badly when what we are really ranking is if it works, if the documentation is good or whatever but not really the performance of the model. And as we do not have A LOT of users, a bad ranking could be really affecting a model.

(Fynn) Do we want model versions on the website? (I think we discussed this before, at least I created this issue before. Would be great to come to a conclusion on it soon.)

(Tomaz) I'd argue we should just use the git model; branch names (animal names for us) move around, so if people want stability, they should reference specific versions, and out APIs should expose (or even require) versions as paramters;
(Iván) I think that it would be usefull for cases such as: I finetunned a model with affabable-shark:1.1, then if a new version comes out (e.g. affabable-shark:1.2) it's good to know wich version was trained with. It would promote retrocompatibility and stability.

(Fynn) Is everyone ok with adding partner community specific teams in our github orga? https://github.com/orgs/bioimage-io/teams
Sometimes it would be nice to tag @ilastik-devs or @deepimagej-devs instead of individual people for issues raised in bioimage-io that (partially) concern a specific tool.

(Caterina) I think it's a great idea! @FynnBe
(Tomaz) Do the community partners be part of the organization in order to be tagged?

(Caterina) Issues needing your attention:

https://github.com/bioimage-io/bioimage.io/issues/437
https://github.com/bioimage-io/bioimage.io/issues/436

(Bea) Please share the Open Call stuff so more people join!

https://www.linkedin.com/posts/ai4life-eu-project_opencall-lifesciences-research-activity-7269712511099183104-ip7c
https://qoto.org/@AI4Life/113589261256336237
https://bsky.app/profile/ai4life.bsky.social/post/3lcfsktfm2c2x
https://x.com/AI4LifeTeam/status/1863947307328167997

Online hackathon.. when can we do this? Prepare for it!

December 11th 2024
Attendees

Name
Affiliation
Username (GitHub)

Anna
EMBL
@akreshuk

Iván Hidalgo
IGC
@IvanHCenalmor