Introduction
cellseg-models.pytorch is a library built upon PyTorch that contains multi-task encoder-decoder architectures along with dedicated post-processing methods for segmenting cell/nuclei instances. As the name might suggest, this library is heavily inspired by segmentation_models.pytorch library for semantic segmentation.
For panoptic segmentation and downstream spatial analysis of whole-slide images, see Histolytics. Histolytics uses cellseg-models.pytorch for its segmentation models.
Features
- Six model families for cell and nuclei instance segmentation.
- Pretrained checkpoints available through CSMP Hub.
- Configurable encoders, decoders and prediction heads.
- Cell-type classification and optional tissue segmentation alongside instance masks.
- Inference on individual images, sliding windows and whole-slide images.
- Datasets, transforms, losses and metrics for training and evaluation.
- ONNX export for all six model families.
Installation
pip install cellseg-models-pytorch
For optional training, ONNX export and OpenSlide installs, see the installation guide.
Read the documentation for the quick start, user guides and API reference.
Quick Start
Initialize a pre-trained model and run inference
pip install cellseg-models-pytorch
pip install albumentations==2.0.8
This checkpoint expects RGB images with pixel values scaled globally to 0–1.
import numpy as np
from albumentations import Normalize, Resize
from cellseg_models_pytorch.models.cellpose import CellPose
from cellseg_models_pytorch.utils import FileHandler
# Initialize a nuclei segmentation model trained on HGSC data.
# see models in https://huggingface.co/csmp-hub
model = CellPose.from_pretrained(weights="hgsc_v1_efficientnet_b5")
model.set_inference_mode()
# Resize to multiple of 32 of your own choosing
resize = Resize(1024, 1024)
normalize = Normalize(normalization="min_max")
im = FileHandler.read_img(IMG_PATH)
# Match the checkpoint's float32 preprocessing before normalization.
im = resize(image=im)["image"].astype(np.float32, copy=False)
im = normalize(image=im)["image"]
prob = model.predict(im)
out = model.post_process(prob)
# out = {"nuc": [(nuc instances (H, W), nuc types (H, W))], "cyto": None, "tissue": None}
Models
Six model families are available. Find pretrained checkpoints on csmp-hub on Hugging Face.
| Model | Paper |
|---|---|
| [1] HoVer-Net | https://www.sciencedirect.com/science/article/pii/S1361841519301045?via%3Dihub |
| [2] Cellpose | https://www.nature.com/articles/s41592-020-01018-x |
| [3] Omnipose | https://www.biorxiv.org/content/10.1101/2021.11.03.467199v2 |
| [4] Stardist | https://arxiv.org/abs/1806.03535 |
| [5] CellVit-SAM | https://arxiv.org/abs/2306.15350 |
| [6] InstanSeg | https://arxiv.org/abs/2408.15954 |
Datasets
Download prepared datasets from CSMP Hub. Each linked dataset card describes its format, labels, splits and license.
| Dataset | Images | Splits | License |
|---|---|---|---|
| [7, 8] PanNuke | 7,901 | fold1, fold2, fold3 |
CC BY-NC-SA 4.0 (noncommercial) |
| [9] PanopTILs Refined | 1,349 | Patient-separated train, val, test |
CC0 1.0 |
| [10] PUMA | 206 | Public challenge train |
CC0 1.0 |
| [11] CytoNuke | 83 | New patient-separated train, val, test |
CC BY 4.0 (CPTAC images: CC BY 3.0) |
| [12] HeLaCytoNuc | 2,676 | Original train, val (automatic labels), test (manual labels) |
CC BY 4.0 |
| [13] AIR-LEISH | 180 | train only; no independent evaluation split |
CC BY 4.0 |
| [14, 15] Lizard-Mitosis | 4,981 | Original train, val, test; train/val overlap |
CC BY-NC-SA 4.0 (noncommercial) |
| [16] Human Lung | 68 | Original train (51), val (7), test (10); patient independence unverified |
CC BY-NC 4.0 (noncommercial) |
| [17, 18, 19] VitaminP ORION-CRC | 3,337 | Original case-separated train (2,946), val (272), test (119) |
CC BY 4.0 |
Load one PanopTILs Refined sample:
from io import BytesIO
import numpy as np
import pyarrow.parquet as pq
from huggingface_hub import hf_hub_download
from PIL import Image
def read_png(data: bytes) -> np.ndarray:
"""Decode RGB pixels or integer labels without reducing mask bit depth."""
with Image.open(BytesIO(data)) as image:
return np.array(image)
path = hf_hub_download(
repo_id="csmp-hub/panoptils_refined",
repo_type="dataset",
filename="train.parquet",
)
row = next(pq.ParquetFile(path).iter_batches(batch_size=1)).to_pylist()[0]
image = read_png(row["image"])
instances = read_png(row["inst"])
cell_types = read_png(row["type"])
tissue_types = read_png(row["sem"])
References
See REFERENCES.md for model papers and dataset sources.
Citation
Please cite the version you used. CITATION.cff provides citation metadata for the software as a whole. The example below cites version 0.1.30.
@misc{lehtonen_cellseg_models_2025,
doi = {10.5281/zenodo.17608242},
url = {https://doi.org/10.5281/zenodo.17608242},
author = {Lehtonen, Oskari},
title = {{cellseg_models.pytorch}},
version = {0.1.30},
publisher = {Zenodo},
year = {2025}
}
Licence
Original code in this project is licensed under MIT. Adapted third-party code retains its original terms. See third-party notices for sources and bundled license texts, including timm, Diffusers, Kornia, MetaFormer, HoVer-Net, Cellpose, StarDist, scikit-image and HistoPrep. Dataset and pretrained-weight licenses are documented separately in their cards.
1 maintainer
Metadata
1 maintainer
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