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hash: .github/workflows/docker-image.yaml:20: update your workflow using https://app.stepsecurity.io/secureworkflow/vanvalenlab/deepcell-spots/docker-image.yaml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/docker-image.yaml:23: update your workflow using https://app.stepsecurity.io/secureworkflow/vanvalenlab/deepcell-spots/docker-image.yaml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/docker-image.yaml:26: update your workflow using https://app.stepsecurity.io/secureworkflow/vanvalenlab/deepcell-spots/docker-image.yaml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/docker-image.yaml:33: update your workflow using https://app.stepsecurity.io/secureworkflow/vanvalenlab/deepcell-spots/docker-image.yaml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/docker-image.yaml:49: update your workflow using https://app.stepsecurity.io/secureworkflow/vanvalenlab/deepcell-spots/docker-image.yaml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/package.yaml:11: update your workflow using https://app.stepsecurity.io/secureworkflow/vanvalenlab/deepcell-spots/package.yaml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/package.yaml:14: update your workflow using https://app.stepsecurity.io/secureworkflow/vanvalenlab/deepcell-spots/package.yaml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/pypi.yaml:16: update your workflow using https://app.stepsecurity.io/secureworkflow/vanvalenlab/deepcell-spots/pypi.yaml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/pypi.yaml:19: update your workflow using https://app.stepsecurity.io/secureworkflow/vanvalenlab/deepcell-spots/pypi.yaml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/pypi.yaml:28: update your workflow using https://app.stepsecurity.io/secureworkflow/vanvalenlab/deepcell-spots/pypi.yaml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/release-drafter.yaml:19: update your workflow using https://app.stepsecurity.io/secureworkflow/vanvalenlab/deepcell-spots/release-drafter.yaml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/tests.yaml:26: update your workflow using https://app.stepsecurity.io/secureworkflow/vanvalenlab/deepcell-spots/tests.yaml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/tests.yaml:29: update your workflow using https://app.stepsecurity.io/secureworkflow/vanvalenlab/deepcell-spots/tests.yaml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/tests.yaml:34: update your workflow using https://app.stepsecurity.io/secureworkflow/vanvalenlab/deepcell-spots/tests.yaml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/tests.yaml:71: update your workflow using https://app.stepsecurity.io/secureworkflow/vanvalenlab/deepcell-spots/tests.yaml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/tests.yaml:72: update your workflow using https://app.stepsecurity.io/secureworkflow/vanvalenlab/deepcell-spots/tests.yaml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/tests.yaml:73: update your workflow using https://app.stepsecurity.io/secureworkflow/vanvalenlab/deepcell-spots/tests.yaml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/tests.yaml:76: update your workflow using https://app.stepsecurity.io/secureworkflow/vanvalenlab/deepcell-spots/tests.yaml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/tests.yaml:104: update your workflow using https://app.stepsecurity.io/secureworkflow/vanvalenlab/deepcell-spots/tests.yaml/master?enable=pin","Warn: containerImage not pinned by hash: Dockerfile:6","Warn: pipCommand not pinned by hash: Dockerfile:20-21","Warn: pipCommand not pinned by hash: Dockerfile:27","Warn: pipCommand not pinned by hash: .github/workflows/tests.yaml:50","Warn: pipCommand not pinned by hash: .github/workflows/tests.yaml:51","Warn: pipCommand not pinned by hash: .github/workflows/tests.yaml:52","Info:   0 out of  10 GitHub-owned GitHubAction dependencies pinned","Info:   0 out of  10 third-party GitHubAction dependencies pinned","Info:   0 out of   1 containerImage dependencies pinned","Info:   0 out of   5 pipCommand dependencies pinned"],"documentation":{"short":"Determines if the project has declared and pinned the dependencies of its build 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vulnerabilities detected","details":["Warn: Project is vulnerable to: GHSA-29gw-9793-fvw7","Warn: Project is vulnerable to: PYSEC-2015-24 / GHSA-4vwq-x64q-j4cj","Warn: Project is vulnerable to: PYSEC-2017-46 / GHSA-66gw-5xpf-gfp5","Warn: Project is vulnerable to: PYSEC-2015-25 / GHSA-92mr-v722-f48m","Warn: Project is vulnerable to: PYSEC-2022-12 / GHSA-pq7m-3gw7-gq5x","Warn: Project is vulnerable to: PYSEC-2017-47","Warn: Project is vulnerable to: PYSEC-2018-34 / GHSA-2fc2-6r4j-p65h","Warn: Project is vulnerable to: PYSEC-2021-856 / GHSA-5545-2q6w-2gh6","Warn: Project is vulnerable to: PYSEC-2019-108 / GHSA-9fq2-x9r6-wfmf","Warn: Project is vulnerable to: PYSEC-2018-33 / GHSA-cw6w-4rcx-xphc","Warn: Project is vulnerable to: PYSEC-2021-857 / GHSA-f7c7-j99h-c22f","Warn: Project is vulnerable to: GHSA-fpfv-jqm9-f5jm","Warn: Project is vulnerable to: PYSEC-2017-1 / GHSA-frgw-fgh6-9g52","Warn: Project is vulnerable to: PYSEC-2020-107 / GHSA-jjw5-xxj6-pcv5","Warn: Project is vulnerable to: PYSEC-2024-110 / GHSA-jw8x-6495-233v","Warn: Project is vulnerable to: PYSEC-2020-108","Warn: Project is vulnerable to: GHSA-2475-53vw-vp25","Warn: Project is vulnerable to: GHSA-27rc-728f-x5w2","Warn: Project is vulnerable to: GHSA-2p9q-h29j-3f5v","Warn: Project is vulnerable to: GHSA-2r2f-g8mw-9gvr","Warn: Project is vulnerable to: GHSA-2vv3-56qg-g2cf","Warn: Project is vulnerable to: GHSA-368v-7v32-52fx","Warn: Project is vulnerable to: GHSA-37jf-mjv6-xfqw","Warn: Project is vulnerable to: GHSA-397c-5g2j-qxpv","Warn: Project is vulnerable to: GHSA-49rq-hwc3-x77w","Warn: Project is vulnerable to: GHSA-4pc4-m9mj-v2r9","Warn: Project is vulnerable to: GHSA-4w68-4x85-mjj9","Warn: Project is vulnerable to: GHSA-54ch-gjq5-4976","Warn: Project is vulnerable to: GHSA-54pp-c6pp-7fpx","Warn: Project is vulnerable to: GHSA-558h-mq8x-7q9g","Warn: Project is vulnerable to: GHSA-5889-7v45-q28m","Warn: Project is vulnerable to: GHSA-5v77-j66x-4c4g","Warn: Project is vulnerable to: GHSA-5w96-866f-6rm8","Warn: Project is vulnerable to: GHSA-5wpj-c6f7-24x8","Warn: Project is vulnerable to: GHSA-647v-r7qq-24fh","Warn: Project is vulnerable to: GHSA-64jg-wjww-7c5w","Warn: Project is vulnerable to: GHSA-66vq-54fq-6jvv","Warn: Project is vulnerable to: GHSA-67pf-62xr-q35m","Warn: Project is vulnerable to: GHSA-689c-r7h2-fv9v","Warn: Project is vulnerable to: GHSA-68v3-g9cm-rmm6","Warn: Project is vulnerable to: GHSA-6hg6-5c2q-7rcr","Warn: Project is vulnerable to: GHSA-6wfh-89q8-44jq","Warn: Project is vulnerable to: GHSA-6x99-gv2v-q76v","Warn: Project is vulnerable to: GHSA-75c9-jrh4-79mc","Warn: Project is vulnerable to: GHSA-762h-vpvw-3rcx","Warn: Project is vulnerable to: GHSA-79h2-q768-fpxr","Warn: Project is vulnerable to: GHSA-7j3m-8g3c-9qqq","Warn: Project is vulnerable to: GHSA-7jvm-xxmr-v5cw","Warn: Project is vulnerable to: GHSA-7x4v-9gxg-9hwj","Warn: Project is vulnerable to: GHSA-828c-5j5q-vrjq","Warn: Project is vulnerable to: GHSA-84jm-4cf3-9jfm","Warn: Project is vulnerable to: GHSA-8fvv-46hw-vpg3","Warn: Project is vulnerable to: GHSA-8w5g-3wcv-9g2j","Warn: Project is vulnerable to: GHSA-8wwm-6264-x792","Warn: Project is vulnerable to: GHSA-93vr-9q9m-pj8p","Warn: Project is vulnerable to: GHSA-94mm-g2mv-8p7r","Warn: Project is vulnerable to: GHSA-97p7-w86h-vcf9","Warn: Project is vulnerable to: GHSA-9942-r22v-78cp","Warn: Project is vulnerable to: GHSA-9cr2-8pwr-fhfq","Warn: Project is vulnerable to: GHSA-9fpg-838v-wpv7","Warn: Project is vulnerable to: GHSA-9j4v-pp28-mxv7","Warn: Project is vulnerable to: GHSA-9v8w-xmr4-wgxp","Warn: Project is vulnerable to: GHSA-9vqj-64pv-w55c","Warn: Project is vulnerable to: GHSA-cg88-rpvp-cjv5","Warn: Project is vulnerable to: GHSA-cqvq-fvhr-v6hc","Warn: Project is vulnerable to: GHSA-cv2p-32v3-vhwq","Warn: Project is vulnerable to: GHSA-cwpm-f78v-7m5c","Warn: Project is vulnerable to: GHSA-f2w8-jw48-fr7j","Warn: Project is vulnerable to: GHSA-f49c-87jh-g47q","Warn: Project is vulnerable to: GHSA-f4rr-5m7v-wxcw","Warn: Project is vulnerable to: GHSA-f4w6-h4f5-wx45","Warn: Project is vulnerable to: GHSA-f637-vh3r-vfh2","Warn: Project is vulnerable to: GHSA-f7r5-q7cx-h668","Warn: Project is vulnerable to: GHSA-ffjm-4qwc-7cmf","Warn: Project is vulnerable to: GHSA-fhfc-2q7x-929f","Warn: Project is vulnerable to: GHSA-fqm2-gh8w-gr68","Warn: Project is vulnerable to: GHSA-fqxc-pvf8-2w9v","Warn: Project is vulnerable to: GHSA-frqp-wp83-qggv","Warn: Project is vulnerable to: GHSA-fv25-wrff-wf86","Warn: Project is vulnerable to: GHSA-fv43-93gv-vm8f","Warn: Project is vulnerable to: GHSA-fxgc-95xx-grvq","Warn: Project is vulnerable to: GHSA-g35r-369w-3fqp","Warn: Project is vulnerable to: GHSA-g468-qj8g-vcjc","Warn: Project is vulnerable to: GHSA-g9fm-r5mm-rf9f","Warn: Project is vulnerable to: GHSA-g9h5-vr8m-x2h4","Warn: Project is vulnerable to: GHSA-gf97-q72m-7579","Warn: Project is vulnerable to: GHSA-gjh7-xx4r-x345","Warn: Project is vulnerable to: GHSA-gq2j-cr96-gvqx","Warn: Project is vulnerable to: GHSA-gw97-ff7c-9v96","Warn: Project is vulnerable to: GHSA-h246-cgh4-7475","Warn: Project is vulnerable to: GHSA-h2wq-prv9-2f56","Warn: Project is vulnerable to: GHSA-h48f-q7rw-hvr7","Warn: Project is vulnerable to: GHSA-h5g4-ppwx-48q2","Warn: Project is vulnerable to: GHSA-h5vq-gw2c-pq47","Warn: Project is vulnerable to: GHSA-h6q3-vv32-2cq5","Warn: Project is vulnerable to: GHSA-h7ff-cfc9-wmmh","Warn: Project is vulnerable to: GHSA-hc2f-7r5r-r2hg","Warn: Project is vulnerable to: GHSA-hq7g-wwwp-q46h","Warn: Project is vulnerable to: GHSA-hrg5-737c-2p56","Warn: Project is vulnerable to: GHSA-hx9q-2mx4-m4pg","Warn: Project is vulnerable to: GHSA-j43h-pgmg-5hjq","Warn: Project is vulnerable to: GHSA-j5w9-hmfh-4cr6","Warn: Project is vulnerable to: GHSA-jjm6-4vf7-cjh4","Warn: Project is vulnerable to: GHSA-jq6x-99hj-q636","Warn: Project is vulnerable to: GHSA-jqm7-m5q7-3hm5","Warn: Project is vulnerable to: GHSA-jvhc-5hhr-w3v5","Warn: Project is vulnerable to: GHSA-m6cv-4fmf-66xf","Warn: Project is vulnerable to: GHSA-m6vp-8q9j-whx4","Warn: Project is vulnerable to: GHSA-mg66-qvc5-rm93","Warn: Project is vulnerable to: GHSA-mgmh-g2v6-mqw5","Warn: Project is vulnerable to: GHSA-mh3m-62v7-68xg","Warn: Project is vulnerable to: GHSA-mv77-9g28-cwg3","Warn: Project is vulnerable to: GHSA-mv8m-8x97-937q","Warn: Project is vulnerable to: GHSA-mw6j-hh29-h379","Warn: Project is vulnerable to: GHSA-p2xf-8hgm-hpw5","Warn: Project is vulnerable to: GHSA-p7hr-f446-x6qf","Warn: Project is vulnerable to: GHSA-p9rc-rmr5-529j","Warn: Project is vulnerable to: GHSA-pf36-r9c6-h97j","Warn: Project is vulnerable to: GHSA-pqhm-4wvf-2jg8","Warn: Project is vulnerable to: GHSA-pxrw-j2fv-hx3h","Warn: Project is vulnerable to: GHSA-q2c3-jpmc-gfjx","Warn: Project is vulnerable to: GHSA-q5jv-m6qw-5g37","Warn: Project is vulnerable to: GHSA-qhw4-wwr7-gjc5","Warn: Project is vulnerable to: GHSA-qjqc-vqcf-5qvj","Warn: Project is vulnerable to: GHSA-qxpx-j395-pw36","Warn: 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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":["biological-data-analysis","deep-learning","spot-detection","tensorflow"],"created_at":"2024-11-09T14:14:55.869Z","updated_at":"2026-04-07T17:31:34.967Z","avatar_url":"https://github.com/vanvalenlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# DeepCell Spots\n\n[![Build Status](https://github.com/vanvalenlab/deepcell-spots/workflows/build/badge.svg)](https://github.com/vanvalenlab/deepcell-spots/actions)\n[![Documentation Status](https://readthedocs.org/projects/deepcell-spots/badge/?version=latest)](https://deepcell-spots.readthedocs.io/en/latest/?badge=latest)\n[![Coverage Status](https://coveralls.io/repos/github/vanvalenlab/deepcell-spots/badge.svg)](https://coveralls.io/github/vanvalenlab/deepcell-spots)\n[![Modified Apache 2.0](https://img.shields.io/badge/license-Modified%20Apache%202-blue)](https://github.com/vanvalenlab/deepcell-spots/blob/master/LICENSE)\n[![PyPI version](https://badge.fury.io/py/DeepCell-Spots.svg)](https://badge.fury.io/py/DeepCell-Spots)\n[![PyPi Monthly Downloads](https://img.shields.io/pypi/dm/deepcell-spots)](https://pypistats.org/packages/deepcell-spots)\n[![Python Versions](https://img.shields.io/pypi/pyversions/deepcell-spots.svg)](https://pypi.org/project/deepcell-spots/)\n\n`deepcell-spots` is a deep learning package for analyzing spatial transcriptomics data sets. Its application, Polaris, allows you to apply pre-existing models and train new deep learning models for fluorescent spot detection. Polaris also contains a probabilistic method for combinatorial barcode assignment. It is written in Python and leverages a number of packages, including: [TensorFlow](https://github.com/tensorflow/tensorflow), [Keras](https://www.tensorflow.org/guide/keras), [PyTorch](https://pytorch.org), and [DeepCell](https://github.com/vanvalenlab/deepcell-tf). More detailed documentation of `deepcell-spots` is available [here](https://deepcell-spots.readthedocs.io/).\n\n# ![Spot Detection Example](/docs/images/spot_montage.png)\n\n# Getting Started\n\n## Install with pip\nThe simplest way to install `deepcell-spots` is with `pip`:\n\n```bash\npip install deepcell-spots\n```\n\n## Install with Docker\nThe `deepcell-spots` Docker container is also available on DockerHub. For more details for running DeepCell Docker containers, please see the [deepcell-tf README](https://github.com/vanvalenlab/deepcell-tf/blob/master/README.md).\n\n\n# DeepCell Spots Applications\n\n`deepcell-spots` contains an applications that greatly simplify the implementation of machine learning models for spot detection and decoding. `SpotDetection` contains a pre-trained model for fluorescent spot detection on images derived from assays such as RNA FISH and in-situ sequencing. This model returns a list of coordinate locations for fluorescent spots detected in the input image. `SpotDecoding` fit a probabilistic model for spot decoding with SVI. It returns a gene identity for each detected spot for multiplex FISH data sets. `Polaris` pairs these two applications with [DeepCell](https://github.com/vanvalenlab/deepcell-tf) models for nuclear and cytoplasmic segmentation. For example implementation, please see the [example notebooks](https://github.com/vanvalenlab/deepcell-spots/blob/master/notebooks).\n\n# DeepCell Spots for Developers\n\nBuild and run a local docker container, similarly to the instructions for deepcell-tf. The relevant parts are copied here with modifications to work for deepcell-spots. For further instructions, see the [deepcell-tf README](https://github.com/vanvalenlab/deepcell-tf/blob/master/README.md).\n\n### Build a local docker container, specifying the deepcell version with DEEPCELL_VERSION\n\nThe deepcell-spots Docker image is built using the deepcell-tf Docker images as a base image, so a ``DEEPCELL_VERSION`` must be specified in the build command.\n\n```bash\ngit clone https://github.com/vanvalenlab/deepcell-spots.git\ncd deepcell-spots\ndocker build --build-arg DEEPCELL_VERSION=0.12.9-gpu -t $USER/deepcell-spots . \n```\n\n### Run the new docker image\n\n```bash\n# '\"device=0\"' refers to the specific GPU(s) to run DeepCell-Spots on, and is not required\ndocker run --gpus '\"device=0\"' -it \\\n-p 8888:8888 \\\n$USER/deepcell-spots\n```\n\nIt can also be helpful to mount the local copy of the repository and the notebooks to speed up local development.\n\n```bash\n# you can now start the docker image with the code mounted for easy editing\ndocker run --gpus '\"device=0\"' -it \\\n    -p 8888:8888 \\\n    -v $PWD/deepcell-spots/deepcell_spots:/usr/local/lib/python3.8/dist-packages/deepcell_spots \\\n    -v $PWD/notebooks:/notebooks \\\n    -v /$PWD:/data \\\n    $USER/deepcell-spots\n```\n\n## Copyright\n\nCopyright © 2019-2024 [The Van Valen Lab](http://www.vanvalen.caltech.edu/) at the California Institute of Technology (Caltech), with support from the Shurl and Kay Curci Foundation, Google Research Cloud, the Paul Allen Family Foundation, \u0026 National Institutes of Health (NIH) under Grant U24CA224309-01.\nAll rights reserved.\n\n## License\n\nThis software is licensed under a modified [APACHE2](https://github.com/vanvalenlab/deepcell-spots/blob/master/LICENSE). See [LICENSE](https://github.com/vanvalenlab/deepcell-spots/blob/master/LICENSE) for full details.\n\n## Trademarks\n\nAll other trademarks referenced herein are the property of their respective owners.\n\n## Credits\n\n[![Van Valen Lab, Caltech](https://upload.wikimedia.org/wikipedia/commons/7/75/Caltech_Logo.svg)](http://www.vanvalen.caltech.edu/)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvanvalenlab%2Fdeepcell-spots","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvanvalenlab%2Fdeepcell-spots","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvanvalenlab%2Fdeepcell-spots/lists"}