{"id":34031756,"url":"https://github.com/janelia-cellmap/dacapo","last_synced_at":"2026-04-01T23:37:50.236Z","repository":{"id":191443033,"uuid":"682737270","full_name":"janelia-cellmap/dacapo","owner":"janelia-cellmap","description":"A framework for easy application of established machine learning techniques on large, multi-dimensional images.","archived":false,"fork":false,"pushed_at":"2025-09-15T19:14:05.000Z","size":57362,"stargazers_count":60,"open_issues_count":30,"forks_count":10,"subscribers_count":4,"default_branch":"main","last_synced_at":"2026-01-07T22:45:11.747Z","etag":null,"topics":["deep-learning","machine-learning","segmentation"],"latest_commit_sha":null,"homepage":"https://janelia-cellmap.github.io/dacapo/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":"funkelab/dacapo","license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/janelia-cellmap.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2023-08-24T20:18:00.000Z","updated_at":"2025-09-15T18:33:59.000Z","dependencies_parsed_at":"2024-03-16T23:42:46.302Z","dependency_job_id":"e9b865f3-3d42-43d0-855e-b00ba824b622","html_url":"https://github.com/janelia-cellmap/dacapo","commit_stats":null,"previous_names":["janelia-cellmap/dacapo"],"tags_count":6,"template":false,"template_full_name":null,"purl":"pkg:github/janelia-cellmap/dacapo","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/janelia-cellmap%2Fdacapo","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/janelia-cellmap%2Fdacapo/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/janelia-cellmap%2Fdacapo/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/janelia-cellmap%2Fdacapo/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/janelia-cellmap","download_url":"https://codeload.github.com/janelia-cellmap/dacapo/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/janelia-cellmap%2Fdacapo/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31292987,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-01T21:15:39.731Z","status":"ssl_error","status_checked_at":"2026-04-01T21:15:34.046Z","response_time":53,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["deep-learning","machine-learning","segmentation"],"created_at":"2025-12-13T18:25:34.034Z","updated_at":"2026-04-01T23:37:50.231Z","avatar_url":"https://github.com/janelia-cellmap.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cimg src=\"https://raw.githubusercontent.com/janelia-cellmap/dacapo/main/docs/source/_static/CellMapLogo.png\" alt=\"CellMap logo\" width=\"85%\"\u003e\n\n# DaCapo ![DaCapo](https://raw.githubusercontent.com/janelia-cellmap/dacapo/main/docs/source/_static/icon_dacapo.png) ![GitHub Org's stars](https://img.shields.io/github/stars/Janelia-cellmap/dacapo)\n\n![PyPI - Downloads](https://img.shields.io/pypi/dm/dacapo-ml)\n[![Documentation Status](https://readthedocs.org/projects/dacapo/badge/?version=stable)](https://dacapo.readthedocs.io/en/stable/?badge=stable)\n![Github Created At](https://img.shields.io/github/created-at/funkelab/dacapo)\n![GitHub License](https://img.shields.io/github/license/janelia-cellmap/dacapo)\n![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2Fjanelia-cellmap%2Fdacapo%2Fmain%2Fpyproject.toml)\n\n[![tests](https://github.com/janelia-cellmap/dacapo/actions/workflows/tests.yaml/badge.svg)](https://github.com/janelia-cellmap/dacapo/actions/workflows/tests.yaml)\n[![black](https://github.com/janelia-cellmap/dacapo/actions/workflows/black.yaml/badge.svg)](https://github.com/janelia-cellmap/dacapo/actions/workflows/black.yaml)\n[![mypy](https://github.com/janelia-cellmap/dacapo/actions/workflows/mypy.yaml/badge.svg)](https://github.com/janelia-cellmap/dacapo/actions/workflows/mypy.yaml)\n[![docs](https://github.com/janelia-cellmap/dacapo/actions/workflows/docs.yaml/badge.svg)](https://janelia-cellmap.github.io/dacapo/)\n[![codecov](https://codecov.io/gh/janelia-cellmap/dacapo/branch/main/graph/badge.svg)](https://codecov.io/gh/janelia-cellmap/dacapo)\n\nA framework for easy application of established machine learning techniques on large, multi-dimensional images.\n\n`dacapo` allows you to configure machine learning jobs as combinations of\n[DataSplits](https://janelia-cellmap.github.io/dacapo/autoapi/dacapo/experiments/datasplits/index.html),\n[Architectures](https://janelia-cellmap.github.io/dacapo/autoapi/dacapo/experiments/architectures/index.html),\n[Tasks](https://janelia-cellmap.github.io/dacapo/autoapi/dacapo/experiments/tasks/index.html),\n[Trainers](https://janelia-cellmap.github.io/dacapo/autoapi/dacapo/experiments/trainers/index.html),\non arbitrarily large volumes of\nmulti-dimensional images. `dacapo` is not tied to a particular learning\nframework, but currently only supports [`torch`](https://pytorch.org/) with\nplans to support [`tensorflow`](https://www.tensorflow.org/).\n\n\n![DaCapo Diagram](https://raw.githubusercontent.com/janelia-cellmap/dacapo/main/docs/source/_static/dacapo_diagram.png)\n\n\n\n## Installation and Setup\nCurrently, python\u003e=3.10 is supported. We recommend creating a new conda environment for dacapo with python 3.10.\n```\nconda create -n dacapo python=3.10\nconda activate dacapo\n```\n\nThen install DaCapo using pip with the following command:\n```\npip install dacapo-ml\n```\nThis will install the minimum required dependencies. \n\nYou may additionally utilize a MongoDB server for storing outputs. To install and run MongoDB locally, refer to the MongoDB documentation [here](https://www.mongodb.com/docs/manual/installation/).\n\nThe use of MongoDB, as well as specifying the compute context (on cluster or not) should be specified in the ```dacapo.yaml``` in the main directory.\n\n## Functionality Overview\n\nTasks we support and approaches for those tasks:\n - Instance Segmentation\n    - Affinities\n    - Local Shape Descriptors\n - Semantic segmentation\n    - Signed distances\n    - One-hot encoding of different types of objects\n\n## Example Tutorial\nA minimal example tutorial can be found in the examples directory and opened in colab here: \u003ca target=\"_blank\" href=\"https://colab.research.google.com/github/janelia-cellmap/dacapo/blob/main/examples/starter_tutorial/minimal_tutorial.ipynb\"\u003e\n  \u003cimg src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/\u003e\n\u003c/a\u003e\n\n## Helpful Resources \u0026 Tools\n - Chunked data, zarr, and n5\n    - OME-Zarr: a cloud-optimized bioimaging file format with international community support (doi: [10.1101/2023.02.17.528834](https://pubmed.ncbi.nlm.nih.gov/36865282/))\n    - Videos about N5 and Fiji can be found in [this playlist](https://www.youtube.com/playlist?list=PLmZHHIZ9Gz-IJA7HtW8quZcuLViz9Em6e). For other questions, join the discussion on the [Image.sc forum](https://forum.image.sc/tag/n5).\n    - Read about chunked storage plugins in Fiji in this blog: [N5 plugins for Fiji](https://openorganelle.janelia.org/news/2023-02-06-n5-plugins-for-fiji)\n    - Script for converting tiff to zarr can be found [here](https://github.com/yuriyzubov/tiff-to-zarr) \n - Segmentations\n    - A description of local shape descriptors used for affinities task. Read the blog [here](https://localshapedescriptors.github.io/). Example image from the blog showing the difference between segmentations:\n    - ![](https://localshapedescriptors.github.io/assets/img/detection_vs_segmentation_neurons.jpeg)\n - CellMap Models\n    - [GitHub Repo](https://github.com/janelia-cellmap/cellmap-models) of published models\n    - For example, the COSEM trained pytorch networks are located [here](https://github.com/janelia-cellmap/cellmap-models/tree/main/src/cellmap_models/pytorch/cosem).\n - [OpenOrganelle.org](https://openorganelle.janelia.org)\n    - ![](https://raw.githubusercontent.com/janelia-cellmap/dacapo/main/docs/source/_static/mito_pred-seg.gif)\n    - Example of [unprocessed distance predictions](https://tinyurl.com/3kw2tuab)\n    - Example of [refined segmentations](https://tinyurl.com/k59pba98) that have undergone post-processing (e.g., thresholding, masking, smoothing)\n    - Example of [groundtruth data](https://tinyurl.com/pu8mespz)\n - Visualization\n    - [Neuroglancer GitHub Repo](https://github.com/google/neuroglancer)\n\n# Citing this repo\nIf you use our code, please cite us and spread the news!\n```\n@article{Patton_DaCapo_a_modular_2024,\nauthor = {Patton, William and Rhoades, Jeff L. and Zouinkhi, Marwan and Ackerman, David G. and Malin-Mayor, Caroline and Adjavon, Diane and Heinrich, Larissa and Bennett, Davis and Zubov, Yurii and Project Team, CellMap and Weigel, Aubrey V. and Funke, Jan},\ndoi = {10.48550/arXiv.2408.02834},\njournal = {arXiv-cs.CV},\ntitle = {{DaCapo: a modular deep learning framework for scalable 3D image segmentation}},\nyear = {2024}\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjanelia-cellmap%2Fdacapo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjanelia-cellmap%2Fdacapo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjanelia-cellmap%2Fdacapo/lists"}