{"id":23412,"library":"cellpose","title":"Cellpose","description":"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.","status":"active","version":"4.1.1","language":"python","source_language":"en","source_url":"https://github.com/MouseLand/cellpose","tags":["segmentation","cell","biomedical-image-analysis","deep-learning","pytorch"],"install":[{"cmd":"pip install cellpose","lang":"bash","label":"PyPI install"}],"dependencies":[{"reason":"Deep learning backend","package":"torch","optional":false},{"reason":"Array operations","package":"numpy","optional":false},{"reason":"Performance for dynamics","package":"numba","optional":false},{"reason":"Image handling","package":"Pillow","optional":false}],"imports":[{"wrong":"from cellpose.models import CellposeModel","symbol":"CellposeModel","correct":"from cellpose import models"}],"quickstart":{"code":"import numpy as np\nfrom cellpose.models import CellposeModel\nmodel = CellposeModel(gpu=True, model_type='cyto')\nimg = np.random.rand(256, 256).astype(np.float32)\nmask, flow, style = model.eval(img, channels=[0,0], diameter=30.0)\nprint(mask.shape)","lang":"python","description":"Loads a pretrained cyto model and segments a random image."},"warnings":[{"fix":"Replace `from cellpose.models import Cellpose` with `from cellpose.models import CellposeModel`.","message":"Cellpose v4 drops the `Cellpose` class and `SizeModel`. Users must use `CellposeModel` for all segmentation.","severity":"breaking","affected_versions":">=4.0.0"},{"fix":"For denoising, use Cellpose 3.x or alternative methods.","message":"Cellpose v4 does not include the denoise module (`cellpose.denoise`).","severity":"breaking","affected_versions":">=4.0.0"},{"fix":"Use `channels=[0,0]` for single-channel grayscale images.","message":"`channels` parameter now expects a list of two integers (channel index, second channel). Passing `None` or single int is deprecated.","severity":"deprecated","affected_versions":">=4.0.0"},{"fix":"Set `torch.backends.mps.is_available()` carefully and consider using CPU or CUDA if artifacts appear.","message":"MPS (Apple Silicon) backend may produce incorrect results with certain operations (e.g., bfloat16).","severity":"gotcha","affected_versions":"all"},{"fix":"Retrain your model using the `CellposeModel` API in v4, or stick to v3 for existing models.","message":"Cellpose models trained in v3.x are not fully compatible with v4.x without retraining.","severity":"gotcha","affected_versions":">=4.0.0"}],"env_vars":null,"search_vec":"'2025':31 '4.1.1':27 'activ':35 'algorithm':11 'analysi':47 'anatom':9 'base':8 'biomed':45 'biomedical-image-analysi':44 'cadenc':33 'carsen':18 'cell':13,43 'cellpos':1,2 'current':24 'deep':5,49 'deep-learn':48 'develop':16 'earli':30 'imag':46 'learn':7,50 'learning-bas':6 'marius':21 'minor':38 'nuclei':15 'pachitariu':22 'per':40 'pytorch':51 'releas':32 'segment':10,42 'sever':37 'stringer':19 'version':25,39 'year':41","created_at":"2026-05-01T08:07:38.443890+00:00","updated_at":"2026-05-01T08:07:38.443890+00:00","problems":{"verify_error":"Traceback (most recent call last):\n  File \"<string>\", line 1, in <module>\n  File \"/tmp/tmplpw6vxlk/venv/lib/python3.12/site-packages/cellpose/models.py\", line 18, in <module>\n    from . import transforms, dynamics, utils, plot\n  File \"/tmp/tmplpw6vxlk/venv/lib/python3.12/site-packages/cellpose/dynam"},"ecosystem":"pypi","meta_description":null,"install_score":null,"quickstart_score":null,"quickstart_tag":null,"pypi_latest":"4.2.1.1","cli_name":"cellpose","cli_version":"","type":"library","homepage":"https://www.cellpose.org","github":"https://github.com/MouseLand/cellpose","docs":null,"changelog":null,"pypi":"https://pypi.org/project/cellpose/","npm":null,"openapi_spec":null,"status_page":null,"smithery":null,"categories":["ai-ml"],"base_url":null,"auth_type":null,"provenance":{"verified_status":"import_fail","verified_at":"2026-07-03","last_verified":"2026-07-03","next_check":"2026-07-10","install_tag":null}}