🔬 Gray Leaf Spot Colony Segmentation — Demo Pipeline

End-to-end analysis pipeline for gray leaf spot (Magnaporthe and related fungal) colony morphometry on 90 mm petri-dish images, powered by a lightweight SmallUNet trained with area-consistency loss (w=0.7).

▶ Try the live demo — upload images, run inference, see overlays & 16 growth charts in your browser.

Model

Weights: rotsl/grayleafspot-segmentation/best_area_w_0.7.pt

Property	Value
Architecture	SmallUNet (custom lightweight U-Net)
Parameters	~250 K
Base channels	16 → 32 → 64 → 128 → 256 (bottleneck)
Input	256 × 256 RGB
Output	1-channel sigmoid mask
Training loss	BCE + area-consistency loss (weight = 0.7)
Dish detection	OpenCV `HoughCircles` on Gaussian-blurred grayscale
CPU compatible	✅ Pure PyTorch — no custom CUDA kernels

SmallUNet Architecture

Input (3 × 256 × 256)
  │
  ├─ enc1: ConvBlock(3 → 16)              ─── skip s1
  ├─ enc2: MaxPool2d → ConvBlock(16 → 32)  ─── skip s2
  ├─ enc3: MaxPool2d → ConvBlock(32 → 64)  ─── skip s3
  ├─ enc4: MaxPool2d → ConvBlock(64 → 128) ─── skip s4
  │
  ├─ bottleneck: MaxPool2d → ConvBlock(128 → 256)
  │
  ├─ up4: Upsample + cat(s4) → ConvBlock(384 → 128)
  ├─ up3: Upsample + cat(s3) → ConvBlock(192 → 64)
  ├─ up2: Upsample + cat(s2) → ConvBlock(96 → 32)
  ├─ up1: Upsample + cat(s1) → ConvBlock(48 → 16)
  │
  └─ head: Conv2d(16 → 1) → Sigmoid

Each ConvBlock = Conv3×3 (no bias) → ReLU → Conv3×3 (no bias) → ReLU. DownBlock = MaxPool2d(2) → ConvBlock. UpBlock = Bilinear upsample(×2, align_corners=False) → cat([skip, x]) → ConvBlock.

Area-Consistency Weights

The model repo contains variants trained with different area-consistency loss weights. Higher weights enforce stronger agreement between predicted mask area and ground-truth polygon area:

Weight file	Loss weight	Description
`best_area_w_0.1.pt`	0.1	Light area regularisation
`best_area_w_0.3.pt`	0.3	Moderate area regularisation
`best_area_w_0.5.pt`	0.5	Balanced BCE + area
`best_area_w_0.7.pt`	0.7	Strong area consistency (used by demo)
`grayleafspot.pt`	—	Main smp.Unet (ResNet-34) model (24.4M params)

Pipeline Overview

┌──────────────────────────────────────────────────────────────────┐
│  Gradio Space (rotsl/grayleafspot-segmentation-demo)             │
│                                                                  │
│  Upload images                                                   │
│  ├─ Fast mode: SmallUNet → mask → overlay (per image)            │
│  └─ Full pipeline (per image):                                   │
│       1. OpenCV HoughCircles → dish detection → px_to_mm         │
│       2. SmallUNet → colony mask (threshold configurable)        │
│       3. Crack detection (adaptive thresholding + morphology)    │
│       4. Hyphae detection (Frangi + Meijering + hybrid skeleton) │
│       5. Morphometrics — all in mm/mm² via per-image calibration │
│       6. 6 overlay panels per image                              │
│       7. 16 growth charts (≥2 images)                            │
│       8. Export: analysis_full.csv / .json / .zip                │
└──────────────────────────────────────────────────────────────────┘

Visualisation Outputs

6 Overlay Panels Per Image

Panel	Colour	Shows
Raw + Dish	Green circle, red contour	Detected dish boundary + colony outline
Colony Mask	White on black	Binary segmentation mask
Colony Overlay	Red 50% blend	Colony area highlighted on raw image
Cracks	Yellow	Detected cracks inside colony (dilated for visibility)
Hyphae	Cyan	Hyphae skeleton (Frangi + Meijering hybrid filter)
All Combined	Red + yellow + cyan	Colony + cracks + hyphae together

16 Growth Charts (when ≥2 images)

All spatial metrics are in mm (or mm²) via per-image px_to_mm calibration from dish detection, so images of different resolutions are correctly comparable.

Category	Charts	Units
Colony geometry	Colony Area, Colony Diameter, Colony Perimeter	mm², mm, mm
Shape descriptors	Eccentricity, Edge Roughness (P/πd), Colony Centre Offset	unitless, unitless, mm
Texture	Colony Texture Entropy, Colony Texture Std Dev	unitless, unitless
Cracks	Crack Area, Crack Coverage, Number of Cracks	mm², %, count
Hyphae	Hyphae Length — Frangi, Meijering, Hybrid	mm, mm, mm
Growth rates	Relative Growth Rate (RGR), Absolute Growth Rate	ln mm²/day, mm²/day

Charts are only generated when ≥2 valid data points exist for that metric. All charts are included as PNGs in the download zip.

Usage via HF API (Programmatic Access)

Run the full pipeline remotely via the Gradio Client without installing anything locally.

Install

pip install gradio_client

Quick Start — Upload + Run Pipeline

from gradio_client import Client, handle_file

client = Client("rotsl/grayleafspot-segmentation-demo")

# Step 1: Upload images
result = client.predict(
    files=[
        handle_file("plate_d01.jpg"),
        handle_file("plate_d03.jpg"),
        handle_file("plate_d05.jpg"),
    ],
    api_name="/on_upload",
)

# Step 2: Run the full analysis pipeline
analysis = client.predict(
    en="GLS_Exp01",               # experiment name
    ed="2026-04-01",              # experiment start date
    un="YourName",                # user name
    pc=1,                         # plates count
    thresh=0.5,                   # mask confidence threshold
    full_pipeline=True,           # enable full morphometrics
    api_name="/on_run",
)

status_msg    = analysis[0]
overlays      = analysis[1]   # list of {image: filepath, caption: str}
charts        = analysis[2]   # list of {image: filepath, caption: str}
results_table = analysis[3]   # {"headers": [...], "data": [[...], ...]}
zip_path      = analysis[4]   # local path to downloaded analysis_full.zip

print(status_msg)
print(f"Overlays: {len(overlays)} panels")
print(f"Charts:   {len(charts)}")
print(f"Download: {zip_path}")

Export Metadata Only (no inference)

meta = client.predict(
    en="GLS_Exp01",
    ed="2026-04-01",
    un="YourName",
    pc=1,
    api_name="/on_export",
)
# meta[0] = status message
# meta[1] = metadata dataframe
# meta[2] = path to image_metadata.zip

Available API Endpoints

Endpoint	Description	Key Parameters
`/on_upload`	Upload images → gallery	`files`: list of filepaths
`/on_sel`	Select image in gallery	`ed`: experiment date
`/on_save`	Save per-image date/reminder	`nd`: date, `nr`: reminder, `ed`: exp date
`/on_export`	Export metadata CSV/JSON/ICS	`en`, `ed`, `un`, `pc`
`/on_run`	Run full pipeline (segmentation + morphometrics + 16 charts)	`en`, `ed`, `un`, `pc`, `thresh`, `full_pipeline`

Batch Processing Script

"""Process a folder of petri dish images via the HF Space API."""
from pathlib import Path
from gradio_client import Client, handle_file

IMAGE_DIR = Path("./my_experiment")
EXPERIMENT = "GLS_Exp01"
START_DATE = "2026-04-01"

client = Client("rotsl/grayleafspot-segmentation-demo")

# Collect all images
images = sorted(
    p for p in IMAGE_DIR.rglob("*")
    if p.suffix.lower() in {".jpg", ".jpeg", ".png", ".tif", ".bmp", ".webp"}
)
print(f"Found {len(images)} images")

# Upload
client.predict(
    files=[handle_file(str(p)) for p in images],
    api_name="/on_upload",
)

# Run pipeline
status, overlays, charts, table, zip_path = client.predict(
    en=EXPERIMENT,
    ed=START_DATE,
    un="BatchUser",
    pc=1,
    thresh=0.5,
    full_pipeline=True,
    api_name="/on_run",
)

print(status)
print(f"Results zip: {zip_path}")

# Access results as a DataFrame
import pandas as pd
df = pd.DataFrame(table["data"], columns=table["headers"])
print(df[["image_path", "area_mm2", "diameter_mm", "crack_coverage_pct"]].to_string())

Output Columns

Metadata

Column	Description
`image_path`	Image filename
`experiment_name`	Experiment identifier
`experiment_date`	Start date (YYYY-MM-DD)
`image_date`	Auto-detected capture date
`day_code`	d01, d02, …
`user_name`	Researcher
`plates_count`	Number of plates

Calibration

Column	Unit	Description
`dish_detected`	bool	Whether dish was found
`dish_radius_px`	px	Dish radius in pixels
`px_to_mm`	mm/px	Per-image scale factor from dish detection
`calibration_diameter_mm`	mm	Should be ≈ 90.0
`calibration_error_pct`	%	Target < 2%

Colony Morphometry

Column	Unit	Description
`area_mm2`	mm²	Colony area
`diameter_mm`	mm	Equivalent circular diameter
`perimeter_mm`	mm	Colony perimeter
`eccentricity`	–	0 = circle, 1 = line
`edge_roughness`	–	Perimeter / equivalent circle perimeter
`centre_delta_mm`	mm	Colony centre to dish centre

Texture

Column	Description
`entropy`	Shannon entropy (local rank filter)
`texture_std`	Pixel intensity standard deviation

Cracks

Column	Unit	Description
`crack_px`	px	Total crack pixels
`crack_area_mm2`	mm²	Total crack area
`crack_coverage_pct`	%	Crack / colony area × 100
`crack_count`	–	Distinct crack count

Hyphae

Column	Unit	Description
`hyph_frangi_mm`	mm	Frangi vesselness skeleton length
`hyph_meijering_mm`	mm	Meijering neuriteness skeleton length
`hyph_hybrid_mm`	mm	Union of both

Time-Series

Column	Unit	Description
`days_since_start`	days	From first image
`rgr_per_day`	day⁻¹	(ln A₂ − ln A₁) / Δdays
`relative_growth_per_day`	mm²/day	(A₂ − A₁) / Δdays

R Studio Integration

library(readr)
library(dplyr)
library(ggplot2)

df <- read_csv("analysis_full.csv")

# Growth curve
df %>%
  filter(is.na(error) | error == "") %>%
  ggplot(aes(x = days_since_start, y = area_mm2, color = experiment_name)) +
  geom_line() + geom_point() +
  labs(x = "Days", y = "Colony Area (mm²)", title = "Gray Leaf Spot Growth") +
  theme_minimal()

# Morphology summary
df %>%
  filter(is.na(error) | error == "") %>%
  group_by(experiment_name) %>%
  summarise(
    n = n(),
    mean_area = mean(area_mm2, na.rm = TRUE),
    mean_roughness = mean(edge_roughness, na.rm = TRUE),
    mean_crack_pct = mean(crack_coverage_pct, na.rm = TRUE),
    total_hyphae = sum(hyph_hybrid_mm, na.rm = TRUE)
  )

# RGR
df %>%
  filter(!is.na(rgr_per_day) & rgr_per_day != "") %>%
  mutate(rgr_per_day = as.numeric(rgr_per_day)) %>%
  ggplot(aes(x = days_since_start, y = rgr_per_day)) +
  geom_col(fill = "steelblue") +
  facet_wrap(~ experiment_name) +
  labs(x = "Days", y = "RGR (day⁻¹)") +
  theme_minimal()

library(jsonlite)
df <- fromJSON("analysis_full.json")

Technical Notes

Per-Image Pixel-to-mm Calibration

Each image gets its own px_to_mm conversion factor derived from dish detection. The pipeline detects the 90 mm petri dish via HoughCircles and computes:

px_to_mm = 90.0 / (2 × dish_radius_px)

This means images of different resolutions (e.g. phone camera vs DSLR vs microscope) are correctly converted to physical mm units independently. If dish detection fails for an image, px_to_mm defaults to 1.0 and dish_detected is set to False.

Segmentation

Resize full image to 256 × 256 → SmallUNet → sigmoid probability map
Threshold at user-configurable confidence level (default 0.5)
Resize mask back to original resolution (nearest-neighbour)

Crack Detection

Local adaptive thresholding (Gaussian, block_size=51) inside colony mask
Filter by elongation: aspect ratio > 2.5 or eccentricity > 0.85
Interior erosion (disk radius 5) to remove edge artefacts

Hyphae Detection

Frangi filter: multi-scale vesselness (σ = 1–4)
Meijering filter: neuriteness (σ = 1–4)
Hybrid: union of both skeletonised responses
Analysis region extends 20 px beyond colony boundary

Troubleshooting

Issue	Fix
Model download fails	Check internet; for gated repos set `HF_TOKEN`
Dish not detected	Full rim must be visible; avoid heavy shadows
Colony not detected	Verify image has visible colony contrast against agar
`px_to_mm = 1.0`	Dish detection failed — check `dish_detected` column
Charts missing	Need ≥2 images with valid data for that metric

Citation

@misc{rohan_r_2026,
    author       = { rohan r },
    title        = { grayleafspot-segmentation-demo (Revision d2b8555) },
    year         = 2026,
    url          = { https://huggingface.co/rotsl/grayleafspot-segmentation-demo },
    doi          = { 10.57967/hf/8569 },
    publisher    = { Hugging Face }
}

License

Apache License 2.0

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