starfish: unified pipelines for image-based transcriptomics

spacetx, updated 🕥 2023-02-11 01:52:24

starfish: scalable pipelines for image-based transcriptomics

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starfish is a Python library for processing images of image-based spatial transcriptomics. It lets you build scalable pipelines that localize and quantify RNA transcripts in image data generated by any FISH method, from simple RNA single-molecule FISH to combinatorial barcoded assays.

  • Starfish enterprise: finding RNA patterns in single cells <https://www.nature.com/articles/d41586-019-02477-9>_, Nature Technology Feature, Aug 2019
  • Developing a Computational Pipeline and Benchmark Datasets for Image-Based Transcriptomics <https://www.ascb.org/science-news/developing-a-computational-pipeline-and-benchmark-datasets-for-image-based-transcriptomics/>_, ASCB Science News, Dec 2018

Documentation

See spacetx-starfish.readthedocs.io <https://spacetx-starfish.readthedocs.io/en/latest/> for the quickstart <https://spacetx-starfish.readthedocs.io/en/latest/gallery/quick_start/plot_quick_start.html>, user guide <https://spacetx-starfish.readthedocs.io/en/latest/user_guide/>, examples <https://spacetx-starfish.readthedocs.io/en/latest/gallery/>, and API <https://spacetx-starfish.readthedocs.io/en/latest/api/>_.

Installation

starfish supports python 3.7 and above and can easily be installed from PyPI:

.. code-block:: bash

$ pip install starfish[napari]

For more detailed installation instructions, see here <https://spacetx-starfish.readthedocs.io/en/latest/installation/>_.

Python Version Notice

starfish will be dropping support for python 3.6 in the next release due to minimum python=3.7 version requirements in upstream dependencies.

Contributing

We welcome contributions from our users! See our contributing.rst_ and developer guide_ for more information.

.. _developer guide: https://spacetx-starfish.readthedocs.io/en/latest/developer_guide/ .. _contributing.rst: https://github.com/spacetx/starfish/blob/master/CONTRIBUTING.rst

Help, support, and questions

Issues

Update installation section in the README.rst and readthedocs.io

opened on 2023-03-14 18:58:56 by shachafl

Curtesy request for the public - Please update the installation section in README.rst and readthedocs.io to clone the repo and pip install in development mode (pip install -e .). The two installation instructions I have followed all refer to pypi which hasn't been updated since May 2021 and is missing a lot of critical fixes: 1) https://spacetx-starfish.readthedocs.io/en/latest/installation/index.html 2) https://github.com/spacetx/starfish#readme

Bump ipython from 8.4.0 to 8.10.0 in /starfish

opened on 2023-02-11 01:52:24 by dependabot[bot]

Bumps ipython from 8.4.0 to 8.10.0.

Commits
  • 15ea1ed release 8.10.0
  • 560ad10 DOC: Update what's new for 8.10 (#13939)
  • 7557ade DOC: Update what's new for 8.10
  • 385d693 Merge pull request from GHSA-29gw-9793-fvw7
  • e548ee2 Swallow potential exceptions from showtraceback() (#13934)
  • 0694b08 MAINT: mock slowest test. (#13885)
  • 8655912 MAINT: mock slowest test.
  • a011765 Isolate the attack tests with setUp and tearDown methods
  • c7a9470 Add some regression tests for this change
  • fd34cf5 Swallow potential exceptions from showtraceback()
  • Additional commits viewable in compare view


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Bump ipython from 7.27.0 to 8.10.0 in /requirements

opened on 2023-02-11 00:12:21 by dependabot[bot]

Bumps ipython from 7.27.0 to 8.10.0.

Commits
  • 15ea1ed release 8.10.0
  • 560ad10 DOC: Update what's new for 8.10 (#13939)
  • 7557ade DOC: Update what's new for 8.10
  • 385d693 Merge pull request from GHSA-29gw-9793-fvw7
  • e548ee2 Swallow potential exceptions from showtraceback() (#13934)
  • 0694b08 MAINT: mock slowest test. (#13885)
  • 8655912 MAINT: mock slowest test.
  • a011765 Isolate the attack tests with setUp and tearDown methods
  • c7a9470 Add some regression tests for this change
  • fd34cf5 Swallow potential exceptions from showtraceback()
  • Additional commits viewable in compare view


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Bump cryptography from 3.4.8 to 39.0.1 in /requirements

opened on 2023-02-08 01:52:51 by dependabot[bot]

Bumps cryptography from 3.4.8 to 39.0.1.

Changelog

Sourced from cryptography's changelog.

39.0.1 - 2023-02-07


* **SECURITY ISSUE** - Fixed a bug where ``Cipher.update_into`` accepted Python
  buffer protocol objects, but allowed immutable buffers. **CVE-2023-23931**
* Updated Windows, macOS, and Linux wheels to be compiled with OpenSSL 3.0.8.

.. _v39-0-0:


39.0.0 - 2023-01-01

  • BACKWARDS INCOMPATIBLE: Support for OpenSSL 1.1.0 has been removed. Users on older version of OpenSSL will need to upgrade.
  • BACKWARDS INCOMPATIBLE: Dropped support for LibreSSL < 3.5. The new minimum LibreSSL version is 3.5.0. Going forward our policy is to support versions of LibreSSL that are available in versions of OpenBSD that are still receiving security support.
  • BACKWARDS INCOMPATIBLE: Removed the encode_point and from_encoded_point methods on :class:~cryptography.hazmat.primitives.asymmetric.ec.EllipticCurvePublicNumbers, which had been deprecated for several years. :meth:~cryptography.hazmat.primitives.asymmetric.ec.EllipticCurvePublicKey.public_bytes and :meth:~cryptography.hazmat.primitives.asymmetric.ec.EllipticCurvePublicKey.from_encoded_point should be used instead.
  • BACKWARDS INCOMPATIBLE: Support for using MD5 or SHA1 in :class:~cryptography.x509.CertificateBuilder, other X.509 builders, and PKCS7 has been removed.
  • BACKWARDS INCOMPATIBLE: Dropped support for macOS 10.10 and 10.11, macOS users must upgrade to 10.12 or newer.
  • ANNOUNCEMENT: The next version of cryptography (40.0) will change the way we link OpenSSL. This will only impact users who build cryptography from source (i.e., not from a wheel), and specify their own version of OpenSSL. For those users, the CFLAGS, LDFLAGS, INCLUDE, LIB, and CRYPTOGRAPHY_SUPPRESS_LINK_FLAGS environment variables will no longer be respected. Instead, users will need to configure their builds as documented here_.
  • Added support for :ref:disabling the legacy provider in OpenSSL 3.0.x<legacy-provider>.
  • Added support for disabling RSA key validation checks when loading RSA keys via :func:~cryptography.hazmat.primitives.serialization.load_pem_private_key, :func:~cryptography.hazmat.primitives.serialization.load_der_private_key, and :meth:~cryptography.hazmat.primitives.asymmetric.rsa.RSAPrivateNumbers.private_key. This speeds up key loading but is :term:unsafe if you are loading potentially attacker supplied keys.
  • Significantly improved performance for :class:~cryptography.hazmat.primitives.ciphers.aead.ChaCha20Poly1305

... (truncated)

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Bump setuptools from 58.1.0 to 65.5.1 in /starfish

opened on 2022-12-27 16:12:48 by dependabot[bot]

Bumps setuptools from 58.1.0 to 65.5.1.

Release notes

Sourced from setuptools's releases.

v65.5.1

No release notes provided.

v65.5.0

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v65.4.1

No release notes provided.

v65.4.0

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v65.3.0

No release notes provided.

v65.2.0

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v65.1.1

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v65.1.0

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v65.0.2

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v65.0.1

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v65.0.0

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v64.0.3

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v64.0.2

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v64.0.1

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v64.0.0

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v63.4.3

No release notes provided.

v63.4.2

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... (truncated)

Changelog

Sourced from setuptools's changelog.

v65.5.1

Misc ^^^^

  • #3638: Drop a test dependency on the mock package, always use :external+python:py:mod:unittest.mock -- by :user:hroncok
  • #3659: Fixed REDoS vector in package_index.

v65.5.0

Changes ^^^^^^^

  • #3624: Fixed editable install for multi-module/no-package src-layout projects.
  • #3626: Minor refactorings to support distutils using stdlib logging module.

Documentation changes ^^^^^^^^^^^^^^^^^^^^^

  • #3419: Updated the example version numbers to be compliant with PEP-440 on the "Specifying Your Project’s Version" page of the user guide.

Misc ^^^^

  • #3569: Improved information about conflicting entries in the current working directory and editable install (in documentation and as an informational warning).
  • #3576: Updated version of validate_pyproject.

v65.4.1

Misc ^^^^

v65.4.0

Changes ^^^^^^^

v65.3.0

... (truncated)

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Bump setuptools from 58.1.0 to 65.5.1 in /requirements

opened on 2022-12-27 15:57:14 by dependabot[bot]

Bumps setuptools from 58.1.0 to 65.5.1.

Release notes

Sourced from setuptools's releases.

v65.5.1

No release notes provided.

v65.5.0

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v65.4.1

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v65.4.0

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v65.3.0

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v65.2.0

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v65.1.1

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v65.1.0

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v65.0.2

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v65.0.1

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v65.0.0

No release notes provided.

v64.0.3

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v64.0.2

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v64.0.1

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v64.0.0

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v63.4.3

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v63.4.2

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... (truncated)

Changelog

Sourced from setuptools's changelog.

v65.5.1

Misc ^^^^

  • #3638: Drop a test dependency on the mock package, always use :external+python:py:mod:unittest.mock -- by :user:hroncok
  • #3659: Fixed REDoS vector in package_index.

v65.5.0

Changes ^^^^^^^

  • #3624: Fixed editable install for multi-module/no-package src-layout projects.
  • #3626: Minor refactorings to support distutils using stdlib logging module.

Documentation changes ^^^^^^^^^^^^^^^^^^^^^

  • #3419: Updated the example version numbers to be compliant with PEP-440 on the "Specifying Your Project’s Version" page of the user guide.

Misc ^^^^

  • #3569: Improved information about conflicting entries in the current working directory and editable install (in documentation and as an informational warning).
  • #3576: Updated version of validate_pyproject.

v65.4.1

Misc ^^^^

v65.4.0

Changes ^^^^^^^

v65.3.0

... (truncated)

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Releases

Release 0.2.2 2021-04-30 23:09:27

  • Updates requirements
  • Updates to documentation
  • Import match_histograms from skimage.exposure
  • Add necessary coords for IntensityTable when using Nearest Neighbors strategy (#1928)
  • Fix localmaxpeakfinder spot_props filter (#1839)

Release 0.2.1 2020-06-18 00:49:10

  • Bump napari to 0.3.4 (#1889)
  • fix how spot_ids are handled by build_traces_sequential and Label._assign() (#1872)
  • reorganized examples gallery and made clarifications to example pipelines and formatting (#1880)
  • added image registration tutorial (#1874)
  • Add assigning spots to cells docs (#1832)
  • Add a Quick Start tutorial (#1869)
  • Update starfish installation guide for JOSS submission (#1868)
  • Add image segmentation docs (#1821)
  • Changing return value of PixelDecoding to DecodedIntensityTable (#1823)
  • Ensure that LocalMaxPeakFinder works in 3D (#1822)
  • Deprecate is_volume parameter with trackpy (#1820)
  • Fix on-demand calculation of BinaryMaskCollection's regionprops (#1819)
  • Remove workaround for non-3D images (#1808)
  • improve from_code_array validation (#1806)
  • Add group_by for tilefetcher-based ImageStack construction (#1796)

Release 0.2.0 2020-01-31 22:06:42

[0.2.0] - 2020-01-31

  • Add level_method to the clip filters. (#1758)
  • adding method to use installed ilastik instance (#1740)
  • Create a TileFetcher-based constructor for ImageStack (#1737)
  • adding mouse v human example to starfish.data (#1741)
  • adding method to binary mask collection that imports labeled images from external sources like ilastik (#1731)
  • Remove starfish.types.Clip (#1729)
  • Move watershed segmentation from morphology.Binarize to morphology.Segment (#1720)
  • Link to the available datasets in "loading data" section (#1722)
  • Document workaround for python3.8 (#1705)
  • Wrap skimage's watershed (#1700)
  • Add 3D support to target assignment. (#1699)
  • Pipeline component and implementation for merging BinaryMaskCollections (#1692)
  • Mechanism to reduce multiple masks into one (#1684)

Release 0.1.10 2019-12-13 18:16:40

[0.1.10] - 2019-12-13

  • Bump slicedimage to 4.1.1 (#1697)
  • Make map/reduce APIs more intuitive (#1686)
  • updates roadmap to reflect 2020H1 plans
  • adding aws scaling vignette (#1638)
  • Use thresholded binarize and mask filtering in existing watershed code. (#1671)
  • adding spot ids to pixel results (#1687)
  • Implement Labeling algorithms (#1680)
  • Thresholded binarize conversion algorithm (#1651)
  • Area filter for binary masks (#1673)
  • Fix stain generation in watershed (#1670)
  • Use the new levels module. (#1669)
  • Linear image leveling (#1666)
  • add axis labels to display() (#1682)
  • Clip method for Richardson Lucy (#1668)
  • Filters for mask collections (#1659)
  • Provide an apply method to binary mask collections. (#1655)
  • adding convience method for slicing codebook data (#1626)
  • Fix display tests and code (#1664)
  • Additional builders for BinaryMaskCollection (#1637)
  • Methods for uncropping binary masks. (#1647)
  • Improve coordinate handling code for BinaryMaskCollection and LabelImage (#1632)

Release - 0.1.9 2019-11-18 17:55:33

  • Create an ArrayLike type (#1649)
  • Verify that binary masks can be generated from empty label images (#1634)
  • Add a morphology package to hold BinaryMaskCollection, LabelImage, and their respective operators (#1631)
  • fixing travis (#1648)
  • Support multiple codewords for the same target (#1646)
  • Update data model for BinaryMaskCollection (#1628)
  • Test for Codebook.to_json / open_json (#1645)
  • Simplify Dockerfile (#1642)
  • Switch to version exclusion for scikit-image workaround (#1629)
  • Clean up binary mask (#1622)
  • adding an extras feild to SpotFindingResults (#1615)
  • deleting Decode and Detect modules in lieu of spot finding refactor (#1598)
  • Fix install issues (#1641)
  • Upgrade to slicedimage 4.1.0 (#1639)
  • Update vocabulary for LabelImage I/O operations. (#1630)
  • Add a label image data type (#1619)
  • Remove deprecated code (#1621)
  • fixing bug with codebook.to_json (#1625)
  • Don't fill a new ImageStack with NaN (#1609)
  • Rename SegmenationMaskCollection to BinaryMaskCollection (#1611)
  • Remove hack to force anonymous memory mapping on osx (#1618)

Release - 0.1.8 2019-10-18 20:11:03

  • Logging improvements (#1617)
  • Make regionprops available per mask (#1610)
  • Don't use mypy 0.740 (#1616)
  • changing test code to use new spot finding modules (#1597)
  • refactoring allen smFish with new spot finding (#1593)
  • clean up max projection (#1379)
  • Use masked fill to produce labeled images (#1582)
  • Replace most instances of starfish.image.Filter.Reduce with imagestack.reduce (#1548)
  • implementing starMap spot finding refactor (#1592)
  • Add slots to classes that subclass xr.DataArray (#1607)
  • Convert SegmentationMaskCollection to a dict-like object (#1579)
  • Test case for multiprocessing + imagestack (#1589)
  • Masked fill method (#1581)
  • Add map/reduce methods to ImageStack (#1539)
  • Unify FunctionSource in Map and Reduce (#1540)
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transcriptomics imaging human-cell-atlas python