napari-fungiform 0.1.0

Napari plugin and CLI for quantifying cell shape and protein distribution on micropatterned substrates.

Fungiform

A napari plugin and CLI for quantifying cell shape and protein distribution on micropatterned substrates. Designed for multi-channel fluorescence confocal images of cells grown on mushroom-shaped fibronectin micropatterns.

Fungiform aligns a canonical pattern template to each image via normalised cross-correlation, warps head / stem / stem-tip sub-regions into image coordinates, segments cells in the cell-border channel, and reports a rich per-cell table of region-based protein intensities, stem-axis geometry, head-region protrusions, and nuclear / cytoplasmic ratios.

Installation

pip install napari-fungiform

Or from source:

git clone https://github.com/lxfhfut/Fungiform.git
cd Fungiform
pip install -e .

Python ≥ 3.10 required.

Quick start

Napari plugin

napari

Then open Plugins → Fungiform. The widget has two sections:

• Single Input — point at a single 4-channel TIFF (merged layout) or a folder containing per-channel siblings *_C0.tif … *_C3.tif (split layout).
• Batch — point at a folder of images; outputs go to <folder>/results/ by default.

CLI

fungiform --dir ./my_images --out ./results

Common flags:

Flag	Default	Effect
--split-channels	off	Inputs are split per channel (*_C0..C3.tif)
--channel-cell	1	1-indexed cell-border channel (e.g. WGA)
--channel-protein	2	Protein-of-interest channel
--channel-nucleus	3	Nucleus channel (e.g. DAPI)
--channel-pattern	4	Pattern channel (e.g. fibronectin)
--ball-radius-fraction	0.25	Rolling-ball radius as fraction of cell's MIC
--no-align	off	Skip NCC alignment (use when no pattern channel)

Run fungiform --help for the full option list.

Output

For each input image MAX_<title>.tif, Fungiform writes into the output directory:

_allResults.csv                          # one row per detected cell
MAX_<title>_Cell_mask.jpg                # labeled segmentation mask
MAX_<title>_mask_overlay.jpg             # cell channel + segmentation overlay
MAX_<title>_image_qc.png                 # 3-panel per-image overview
qc_cells/<Label>_qc.png                  # 6-panel per-cell QC
protrusions/<Label>_protrusions.png      # per-cell protrusion detail
protrusions/MAX_<title>_protrusions.png  # rolling-ball multi-cell detail
protrusions/MAX_<title>_protrusions_overview.png

See docs/Results_interpretations.md for a column-by-column description of _allResults.csv and a panel-by-panel guide to every visualisation.

Pattern templates

Fungiform ships with default mushroom-pattern templates (perfect / head / stem) under src/fungiform/templates/. To use your own pattern shape, supply --pattern-template, --head-template, and --stem-template pointing at TIFF masks.

Citation

If you use Fungiform in your research, please cite this repository:

@software{fungiform,
  author = {Lin, Xufeng},
  title  = {Fungiform: Napari plugin for micropattern cell quantification},
  url    = {https://github.com/lxfhfut/Fungiform},
  year   = {2026}
}

License

BSD 3-Clause — see LICENSE.