cistardist-pytorch 0.3.0

PyTorch-only StarDist 2D inference for Keras H5 StarDist weights.

cistardist_pytorch

PyTorch-only StarDist 2D inference for existing TensorFlow/Keras StarDist .h5 weights. The first target model is models/SD_Nuclei_Versatile.

This repo intentionally does not depend on TensorFlow, Keras, CSBDeep, or the upstream stardist Python package.

Install

The package is published on PyPI: https://pypi.org/project/cistardist-pytorch/

Install the library with:

pip install cistardist-pytorch

PyTorch is intentionally not pinned by the package, so you can choose the CPU or CUDA build that matches your environment. For this repo's CUDA 12.6 setup, use:

conda create -n cistardist_pytorch python=3.10
conda activate cistardist_pytorch
pip install -r requirements.txt
pip install -e . --no-deps

The package includes a compiled StarDist-style C++ NMS extension for fast polygon suppression. When building from source, a C++ compiler is needed to compile it; if the extension is not available, inference automatically falls back to the slower pure-Python NMS implementation. See COMPILE_NMS.md for detailed build instructions.

Convert and Predict

cistardist-convert models/SD_Nuclei_Versatile
cistardist-predict models/SD_Nuclei_Versatile data/nuclei.tif --out outputs/nuclei_labels.tif

The converter reads config.json, thresholds.json, and weights_best.h5. It writes a PyTorch checkpoint next to the source model as weights_best.pt.

Python API

import tifffile
from cistardist_pytorch import StarDist2D

model = StarDist2D.from_folder("models/SD_Nuclei_Versatile")
image = tifffile.imread("data/nuclei.tif")
labels, details = model.predict_instances(image)

Current Scope

• 2D grayscale inference
• Keras .h5 Conv2D weight conversion via h5py
• StarDist-style polygon postprocessing with compiled C++ NMS and vendored BSD-compatible 2D geometry
• No training, no TensorFlow reference tests, no 3D, no multiclass models

Attribution

The 2D geometry and NMS behavior follows the BSD-3-Clause upstream StarDist project: https://github.com/stardist/stardist