Single-cell pattern U-Net (single-cell-pattern-unet)

Small dense foreground / background segmenter for LISCA micropattern brightfield ROI crops (~128×128 single-cell sites).

Use it whenever you need a binary cell mask on a patterned site (gene-expression intensity, binding overlays, etc.) without running full Cellpose cpsam.

Published as: keejkrej/single-cell-pattern-unet

Why not full Cellpose cpsam?

cpsam (ViT-L, 304M) is excellent as a teacher for pseudo-labels, but production masks only need binary foreground for intensity / area metrics. This student U-Net (1.9M params, ~7.4 MB ONNX) is distilled from cpsam labels on in-house TF84 BF frames.

Teacher weights are CC-BY-NC; this student is trained on your images only.

Files

onnx/model.onnx       # inference graph
export_meta.json      # preprocess / postprocess contract
README.md

Local checkout path in the lisca monorepo is still models/gene-expression-fg-unet/ (historical); the Hugging Face id is the canonical name.

Metrics (TF84 hold-out positions)

Split	Samples	Best val Dice
train	41,548	—
val	6,990	0.888 (epoch 18)

Teacher: Cellpose v4 cpsam, time stride 20, empty masks dropped (fg < 0.1%).

Preprocess / postprocess

Matches export_meta.json:

1. Min–max normalize BF crop → uint8
2. Resize to 128×128
3. Grayscale → RGB, ImageNet mean/std
4. ONNX logits (N,1,128,128) → sigmoid ≥ 0.5
5. Nearest resize to original H×W, hole fill

ONNX I/O

	Name	Shape
input	pixel_values	(N, 3, 128, 128) float32
output	logits	(N, 1, 128, 128) float32

Inference (lisca Rust)

# download
huggingface-cli download keejkrej/single-cell-pattern-unet \
  --local-dir ./models/gene-expression-fg-unet

export LISCA_GE_SEG_MODEL=./models/gene-expression-fg-unet/onnx
lisca-analyze segment ~/data/TF84 --backend onnx --force

Train (from lisca/python)

cd python && uv sync --group train

uv run lisca dataset label-cpsam \
  --workspace ~/data/TF84 --output ~/data/TF84/cpsam_labels \
  --channel 0 --time-stride 20

uv run lisca dataset create-gene-expression-seg \
  --labels ~/data/TF84/cpsam_labels --output ~/data/TF84/ge_seg_dataset

uv run lisca dataset train-gene-expression-seg \
  --dataset ~/data/TF84/ge_seg_dataset --output ~/data/TF84/ge_seg_runs \
  --epochs 40 --image-size 128

Env

Variable	Meaning
LISCA_GE_SEG_MODEL	Directory containing model.onnx (or path to the file)