cellpose

library4.2.1.1pypypiunverified

Cellpose is a deep learning-based anatomical segmentation algorithm for cells and nuclei, developed by Carsen Stringer and Marius Pachitariu. The current version is 4.1.1 (as of early 2025). Release cadence is active with several minor versions per year.

ai-ml

pip install cellpose

github ↗package ↗homepage ↗

INSTALL

IMPORT

SIG · CELLPOSE

cellpose

ai-mlpythonv4.2.1.1

Install

74.8s avg

Import

—

Disk

5325MB

Pass rate

4/ 10

Env Coverage4 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v4.2.1.1 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

glibc

py 3.10

✕ build_error

✓ 84s

py 3.11

✕ build_error

✓ 78.3s

py 3.12

✕ build_error

✓ 69.2s

py 3.13

✕ build_error

✓ 67.7s

py 3.9

✕ build_error

✕ timeout

5325MB installed

● package 5325MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

CellposeModel

✓ from cellpose import models

✗ from cellpose.models import CellposeModel

Loads a pretrained cyto model and segments a random image.

import numpy as np from cellpose.models import CellposeModel model = CellposeModel(gpu=True, model_type='cyto') img = np.random.rand(256, 256).astype(np.float32) mask, flow, style = model.eval(img, channels=[0,0], diameter=30.0) print(mask.shape)

cellpose --version

Debug

Known issues

breakingCellpose v4 drops the `Cellpose` class and `SizeModel`. Users must use `CellposeModel` for all segmentation.

fix

Replace `from cellpose.models import Cellpose` with `from cellpose.models import CellposeModel`.

affects: >=4.0.0

breakingCellpose v4 does not include the denoise module (`cellpose.denoise`).

fix

For denoising, use Cellpose 3.x or alternative methods.

affects: >=4.0.0

deprecated`channels` parameter now expects a list of two integers (channel index, second channel). Passing `None` or single int is deprecated.

fix

Use `channels=[0,0]` for single-channel grayscale images.

affects: >=4.0.0

gotchaMPS (Apple Silicon) backend may produce incorrect results with certain operations (e.g., bfloat16).

fix

Set `torch.backends.mps.is_available()` carefully and consider using CPU or CUDA if artifacts appear.

affects: all

gotchaCellpose models trained in v3.x are not fully compatible with v4.x without retraining.

fix

Retrain your model using the `CellposeModel` API in v4, or stick to v3 for existing models.

affects: >=4.0.0

Upgrade

Version history

4.2.1.1latest on PyPI · released Jun 14, 2026

Audit

Dependencies

torchrequiredDeep learning backend

numpyrequiredArray operations

numbarequiredPerformance for dynamics

PillowrequiredImage handling

Agent activity

22 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/MouseLand/cellpose ↗

packagehttps://pypi.org/project/cellpose/ ↗

homepagehttps://www.cellpose.org ↗