Tags: BioMeDS/starfish
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Tag 0.3.2 - Updating CHANGELOG.md for release 0.3.2 - Bump cryptography from 44.0.0 to 44.0.1 in /requirements (spacetx#2051) - rolling back to Sphinx v5 as v6-8 introduce issues on ReadTheDocs with navbar logo and sub-menus (spacetx#2050) - Scikit image update from 0.21 to 0.23+ (spacetx#2049) - Bump jinja2 from 3.1.4 to 3.1.5 in /requirements (spacetx#2048) - Missing pypi description fix by adding pyproject.toml (spacetx#2047) - Bump actions/setup-python from 2 to 5 (spacetx#2042) - Bump actions/cache from 2 to 4 (spacetx#2041) - Bump actions/checkout from 2 to 4 (spacetx#2040) - Create dependabot.yml to auto update Github Action versions (spacetx#2039) - Bump tornado from 6.4.1 to 6.4.2 in /requirements (spacetx#2038) - replace scipy.ndimage.filters with scipy.ndimage for scipy v2 (spacetx#2035) - Bump lxml-html-clean from 0.3.1 to 0.4.0 in /requirements (spacetx#2036) - Dropping support for Python 3.8 and setting Python 3.9 as minimum (spacetx#2018) - Update readthedocs.yml (spacetx#2014) - Scripts and dependencies updates for Python 3.8 - 3.10 (spacetx#2009) - Add min_distance parameter to peak_local_max call (spacetx#2008) - Various Small Fixes/Improvements (spacetx#1985) - Updated seqFISH Decoding Method: CheckAll Decoder (spacetx#1978) - Bump dask from 2021.9.0 to 2021.10.0 in /requirements (spacetx#1968) - Revert "Revert "Fix coords assignment in CombineAdjustFeatures.run (spacetx#1965)" (spacetx#1966)" (spacetx#1967) - Revert "Fix coords assignment in CombineAdjustFeatures.run (spacetx#1965)" (spacetx#1966) - Fix coords assignment in CombineAdjustFeatures.run (spacetx#1965) - Add to_dict and from_dict methods to TransformsList class (spacetx#1956) - fix notebook tests - Fix check-notebooks makefile command; Add python 3.9 to slow-tests - Fix Sphinx docs - Register pytest markers - Remove is_volume param from testing TrackpyLocalMaxPeakFinder invocation - Address skimage deprecation of skimage.morphology.watershed - Address Xarray pending deprecation for GroupBy.apply - Remove usage of deprecated numpy builtin types like np.bool/np.int - Add n_processes parameter to FindSpotsAlgorithm.run() abstract method - Remove deprecated `indices` param for skimage.feature.peak_local_max - Resolve failure when `peak_local_max()` finds no spots - Fix failing nearest neighbor trace builder tests - Fix composite codebook decoder tests - Change default value of BlobDetector exclude_border parameter to False - Fix incorrect type annotation and improper `.data()` method call - Fix failing morphology utility functions - Fix failing LearnTransform Translation class - Fix failing Codebook and IntensityTable shape validator - Fix failing Codebook.decode_per_round_max() test - Update .gitignore file - Defer when docker-smoketest github actiosn job is run - Bump requirements to clear github actions cache - Fix broken github actions Lint job; Fix broken caching - Address Mypy type annotation errors - Update github actions to use caching; Disable Napari tests for now - Use `python -m pip install ...` to perform pip upgrade - Replace Travis CI with Github Actions - Bump napari to 0.3.4 (spacetx#1889) - fix how spot_ids are handled by build_traces_sequential and Label._assign() (spacetx#1872) - reorganized examples gallery and made clarifications to example pipelines and formatting (spacetx#1880) - added image registration tutorial (spacetx#1874) - Add assigning spots to cells docs (spacetx#1832) - Add a Quick Start tutorial (spacetx#1869) - Update starfish installation guide for JOSS submission (spacetx#1868) - Add image segmentation docs (spacetx#1821) - Changing return value of PixelDecoding to DecodedIntensityTable (spacetx#1823) - Ensure that LocalMaxPeakFinder works in 3D (spacetx#1822) - Deprecate is_volume parameter with trackpy (spacetx#1820) - Fix on-demand calculation of BinaryMaskCollection's regionprops (spacetx#1819) - Remove workaround for non-3D images (spacetx#1808) - improve from_code_array validation (spacetx#1806) - Add group_by for tilefetcher-based ImageStack construction (spacetx#1796) - Bump slicedimage to 4.1.1 (spacetx#1697) - Make map/reduce APIs more intuitive (spacetx#1686) - updates roadmap to reflect 2020H1 plans - adding aws scaling vignette (spacetx#1638) - Use thresholded binarize and mask filtering in existing watershed code. (spacetx#1671) - adding spot ids to pixel results (spacetx#1687) - Implement Labeling algorithms (spacetx#1680) - Thresholded binarize conversion algorithm (spacetx#1651) - Area filter for binary masks (spacetx#1673) - Fix stain generation in watershed (spacetx#1670) - Use the new levels module. (spacetx#1669) - Linear image leveling (spacetx#1666) - add axis labels to display() (spacetx#1682) - Clip method for Richardson Lucy (spacetx#1668) - Filters for mask collections (spacetx#1659) - Provide an apply method to binary mask collections. (spacetx#1655) - adding convience method for slicing codebook data (spacetx#1626) - Fix display tests and code (spacetx#1664) - Additional builders for BinaryMaskCollection (spacetx#1637) - Methods for uncropping binary masks. (spacetx#1647) - Improve coordinate handling code for BinaryMaskCollection and LabelImage (spacetx#1632) - Logging improvements (spacetx#1617) - Make regionprops available per mask (spacetx#1610) - Don't use mypy 0.740 (spacetx#1616) - changing test code to use new spot finding modules (spacetx#1597) - refactoring allen smFish with new spot finding (spacetx#1593) - clean up max projection (spacetx#1379) - Use masked fill to produce labeled images (spacetx#1582) - Replace most instances of starfish.image.Filter.Reduce with imagestack.reduce (spacetx#1548) - implementing starMap spot finding refactor (spacetx#1592) - Add __slots__ to classes that subclass xr.DataArray (spacetx#1607) - Convert SegmentationMaskCollection to a dict-like object (spacetx#1579) - Test case for multiprocessing + imagestack (spacetx#1589) - Masked fill method (spacetx#1581) - Add map/reduce methods to ImageStack (spacetx#1539) - Unify FunctionSource in Map and Reduce (spacetx#1540) - Switch to python multithreading (spacetx#1544) - Don't waste memory/compute in preserve_float_range (spacetx#1545) - Get rid of shared state for LocalMaxPeakFinder (spacetx#1541) - map filter (spacetx#1520) - funcs passed to apply and transform can use positional arguments (spacetx#1519) - import SegmentationMaskCollection in main starfish (spacetx#1527) - Enable Windows builds on master (spacetx#1538) - Throw a warning when the data size is unusual. (spacetx#1525) - Update in-place experiment writing to use the new WriterContract API in slicedimage 4.0.0 (spacetx#1447) - data set formatter with fixed filenames (spacetx#1421) - Refactor reduce to take an optional module and only a function name. (spacetx#1386) - Codify the expectation that in-place experiment construction does not rely on TileFetcher data (spacetx#1389) - Warn and return empty SpotAttributes when PixelDecoding finds 0 spots (spacetx#1400) - updating data.merfish link to full dataset (spacetx#1406) - Rename tile_coordinates to tile_identifier (spacetx#1401) - Support for irregular images in the builder (spacetx#1382) - Fix how we structure the run notebook rules. (spacetx#1384) - updated loading data docs and added image of napari viewer (spacetx#1387) - Format complete ISS experiment and expose in starfish.data (spacetx#1316) - Add concatenate method for ExpressionMatrix (spacetx#1381) - Add TransformsList __repr__ (spacetx#1380) - Fix 3d smFISH notebook as well. (spacetx#1385) - Add custom clip Filter classes (spacetx#1376) - Fix smFISH notebook. (spacetx#1383) - Add Filter.Reduce (general dimension reduction for ImageStack) (spacetx#1342) - Handle denormalized numbers when normalizing intensities/codebooks (spacetx#1371) - TileFetcher formats complete 496 fov MERFISH dataset (spacetx#1341) - Refactor fov.getImage() to fov.getImages() (spacetx#1346) - Add the ability to write labeled experiments (spacetx#1374) - Add inplace TileFetcher module back to public builder API (spacetx#1375) - Always create Z coordinates, even on 4D datasets. (spacetx#1358) - Create an all-purpose ImageStack factory (spacetx#1348) - Remove physical_coordinate_calculator.py (spacetx#1352) - ImageStack parsers should provide coordinates as an array (spacetx#1351) - bump to slicedimage 3.1.1 (spacetx#1343) - Creating a standard starfish.wdl that can be run with any recipe file (spacetx#1364) - public/private separation (spacetx#1244) - Recipe and recipe execution (spacetx#1192) - 3d smFISH notebook (spacetx#1238) - SeqFISH notebook (spacetx#1239) - Adding windows install instructions (spacetx#1227) - vectorize labeling spot lookups (spacetx#1215) - vectorize imagestack -> intensity_table coordinate transfer (spacetx#1212) - Fix the restoration of non-indexed axes. (spacetx#1189) - Allow for intensity tables with labeled axes (spacetx#1181) - ImageStack select on Physical Coordinates (spacetx#1147) - fixing Clip.SCALE_BY_IMAGE (spacetx#1193) - Update BaristaSeq text, fix LinearUnmixing (spacetx#1188) - Update STARmap notebook for SpaceJam (spacetx#1199) - replace label images with segmentation masks (spacetx#1135) - BaristaSeq + Plot tools update (spacetx#1171) - Intensity Table Concat Processing (spacetx#1118) - Transfer physical Coords to Expression Matrix (spacetx#965) - Support for hierarchical directory structures for experiments. (spacetx#1126) - Pipeline Components: LearnTransform and ApplyTransform (spacetx#1083) - Restructure the relationship between PipelineComponent and AlgorithmBase (spacetx#1095) - Last release without a changelog! [0.3.2]: https://github.com/spacetx/starfish/releases/tag/0.3.2 [0.3.1]: https://github.com/spacetx/starfish/releases/tag/0.3.1 [0.3.0]: https://github.com/spacetx/starfish/releases/tag/0.3.0 [0.2.2]: https://github.com/spacetx/starfish/releases/tag/0.2.2 [0.2.1]: https://github.com/spacetx/starfish/releases/tag/0.2.1 [0.2.0]: https://github.com/spacetx/starfish/releases/tag/0.2.0 [0.1.10]: https://github.com/spacetx/starfish/releases/tag/0.1.10 [0.1.9]: https://github.com/spacetx/starfish/releases/tag/0.1.9 [0.1.8]: https://github.com/spacetx/starfish/releases/tag/0.1.8 [0.1.7]: https://github.com/spacetx/starfish/releases/tag/0.1.7 [0.1.6]: https://github.com/spacetx/starfish/releases/tag/0.1.6 [0.1.5]: https://github.com/spacetx/starfish/releases/tag/0.1.5 [0.1.4]: https://github.com/spacetx/starfish/releases/tag/0.1.4 [0.1.3]: https://github.com/spacetx/starfish/releases/tag/0.1.3 [0.1.2]: https://github.com/spacetx/starfish/releases/tag/0.1.2 [0.1.1]: https://github.com/spacetx/starfish/releases/tag/0.1.1 [0.1.0]: https://github.com/spacetx/starfish/releases/tag/0.1.0 [0.0.36]: https://github.com/spacetx/starfish/releases/tag/0.0.36 [0.0.35]: https://github.com/spacetx/starfish/releases/tag/0.0.35 [0.0.34]: https://github.com/spacetx/starfish/releases/tag/0.0.34 [0.0.33]: https://github.com/spacetx/starfish/releases/tag/0.0.33
Tag 0.3.1 - Updating CHANGELOG.md for release 0.3.1 - Adding support to Python 3.12 (spacetx#2027) - Numpy 1.26 update to support Python 3.12 (spacetx#2025) - fixing blob radius calculation in 2d (spacetx#2023) - Release 0.3.0 (spacetx#2021) - Updates requirements - Updates to documentation - Import match_histograms from skimage.exposure - Add necessary coords for IntensityTable when using Nearest Neighbors strategy (spacetx#1928) - Fix localmaxpeakfinder spot_props filter (spacetx#1839) - Add level_method to the clip filters. (spacetx#1758) - adding method to use installed ilastik instance (spacetx#1740) - Create a TileFetcher-based constructor for ImageStack (spacetx#1737) - adding mouse v human example to starfish.data (spacetx#1741) - adding method to binary mask collection that imports labeled images from external sources like ilastik (spacetx#1731) - Remove starfish.types.Clip (spacetx#1729) - Move watershed segmentation from morphology.Binarize to morphology.Segment (spacetx#1720) - Link to the available datasets in "loading data" section (spacetx#1722) - Document workaround for python3.8 (spacetx#1705) - Wrap skimage's watershed (spacetx#1700) - Add 3D support to target assignment. (spacetx#1699) - Pipeline component and implementation for merging BinaryMaskCollections (spacetx#1692) - Mechanism to reduce multiple masks into one (spacetx#1684) - Create an ArrayLike type (spacetx#1649) - Verify that binary masks can be generated from empty label images (spacetx#1634) - Add a morphology package to hold BinaryMaskCollection, LabelImage, and their respective operators (spacetx#1631) - fixing travis (spacetx#1648) - Support multiple codewords for the same target (spacetx#1646) - Update data model for BinaryMaskCollection (spacetx#1628) - Test for Codebook.to_json / open_json (spacetx#1645) - Simplify Dockerfile (spacetx#1642) - Switch to version exclusion for scikit-image workaround (spacetx#1629) - Clean up binary mask (spacetx#1622) - adding an extras feild to SpotFindingResults (spacetx#1615) - deleting Decode and Detect modules in lieu of spot finding refactor (spacetx#1598) - Fix install issues (spacetx#1641) - Upgrade to slicedimage 4.1.0 (spacetx#1639) - Update vocabulary for LabelImage I/O operations. (spacetx#1630) - Add a label image data type (spacetx#1619) - Remove deprecated code (spacetx#1621) - fixing bug with codebook.to_json (spacetx#1625) - Don't fill a new ImageStack with NaN (spacetx#1609) - Rename SegmenationMaskCollection to BinaryMaskCollection (spacetx#1611) - Remove hack to force anonymous memory mapping on osx (spacetx#1618) - ISS refactored with new spot finding path (spacetx#1518) - Fix bugs in per-round-max-decoder (spacetx#1602) - Fix dimension ordering on Codebook and IntensityTable (spacetx#1600) - provanance logging refactor and support for SpotFindingResults (spacetx#1517) - napari 0.2.0 release (spacetx#1599) - starfish.display: unpin napari version, add tests, view masks separately (spacetx#1570) - adding coordinate support to SpotFindingResults (spacetx#1516) - adding new SpotFindingResults data structure and new packages (spacetx#1515) - Update the documentation for data formatters (spacetx#1476) - add ability to convert segmentation masks to a label image - If in_place=True, we should return None (spacetx#1473) - downgrade pyparsing (spacetx#1467) - fixes unicode in issue template (spacetx#1464) - Adds issue templates (spacetx#1460) - Updating requirements. (spacetx#1461) - Bump to slicedimage 4.0.1 (spacetx#1458) - on-demand loading of data. (spacetx#1456) - Get rid of the check-requirements cron job. (spacetx#1448) - Fixing travis build (spacetx#1457) - removing duplicate file (spacetx#1455) - Remove Cli (spacetx#1444) - Instantiate the multiprocessing pool using `with` (spacetx#1436) - Slight optimization of pixel decoding (spacetx#1412) - [easy] point starfish.data.osmFISH() to new dataset (spacetx#1425) - [easy] Warn about the deprecation of the MaxProject filter (spacetx#1390) - [Easy] Fixing spot detection for labeled axes (spacetx#1347) - Schema versioning (spacetx#1278) - Add a missing parameter to wrapper for trackpy local max peak finder (spacetx#1300) - Fix physical coordinate calculator (spacetx#1350) - Fix spot detection for labeled data. (spacetx#1349) - Adding back ability to crop on fov.get_image() (spacetx#1329) - RFC: Base calling filter for in situ sequencing (spacetx#1281) - Preserve subpixel offsets from spot detection (spacetx#1330) - Update strict requirements (spacetx#1142) - High level goal: detect spots should accept imagestacks and not numpy arrays. (spacetx#1143) - Remove cropping from PixelSpotDetector, (spacetx#1120) - Add LocalSearchBlobDetector to support BaristaSeq, SeqFISH, STARmap (spacetx#1074) - Indirect File click types (spacetx#1124) - Move the registration tests next to their sources. (spacetx#1134) - Test to verify that inplace experiment construction works. (spacetx#1131) - Additional support code for building experiments in-place. (spacetx#1127) - Adding ability to pass aligned group to Imagestack.from_path_or_url (spacetx#1069) - Add Decoded Spot Table (spacetx#1087) - Enable appending to existing napari viewer in display() (spacetx#1093) - Change tile shape to a dict by default (spacetx#1072) - Add ElementWiseMult Filter Pipeline Component (spacetx#983) - Add linear unmixing pipeline component (spacetx#1056) - Spiritual Bag of Images Refactor: Part 1 (spacetx#986) - Add to provenance log (spacetx#968)
Tag 0.2.2 - Updates requirements - Updates to documentation - Import match_histograms from skimage.exposure - Add necessary coords for IntensityTable when using Nearest Neighbors strategy (spacetx#1928) - Fix localmaxpeakfinder spot_props filter (spacetx#1839)
Tag 0.2.1 - Bump napari to 0.3.4 (spacetx#1889) - fix how spot_ids are handled by build_traces_sequential and Label._assign() (spacetx#1872) - reorganized examples gallery and made clarifications to example pipelines and formatting (spacetx#1880) - added image registration tutorial (spacetx#1874) - Add assigning spots to cells docs (spacetx#1832) - Add a Quick Start tutorial (spacetx#1869) - Update starfish installation guide for JOSS submission (spacetx#1868) - Add image segmentation docs (spacetx#1821) - Changing return value of PixelDecoding to DecodedIntensityTable (spacetx#1823) - Ensure that LocalMaxPeakFinder works in 3D (spacetx#1822) - Deprecate is_volume parameter with trackpy (spacetx#1820) - Fix on-demand calculation of BinaryMaskCollection's regionprops (spacetx#1819) - Remove workaround for non-3D images (spacetx#1808) - improve from_code_array validation (spacetx#1806) - Add group_by for tilefetcher-based ImageStack construction (spacetx#1796)
Tag 0.2.0 - Add level_method to the clip filters. (spacetx#1758) - adding method to use installed ilastik instance (spacetx#1740) - Create a TileFetcher-based constructor for ImageStack (spacetx#1737) - adding mouse v human example to starfish.data (spacetx#1741) - adding method to binary mask collection that imports labeled images from external sources like ilastik (spacetx#1731) - Remove starfish.types.Clip (spacetx#1729) - Move watershed segmentation from morphology.Binarize to morphology.Segment (spacetx#1720) - Link to the available datasets in "loading data" section (spacetx#1722) - Document workaround for python3.8 (spacetx#1705) - Wrap skimage's watershed (spacetx#1700) - Add 3D support to target assignment. (spacetx#1699) - Pipeline component and implementation for merging BinaryMaskCollections (spacetx#1692) - Mechanism to reduce multiple masks into one (spacetx#1684)
Tag 0.1.10 - Bump slicedimage to 4.1.1 (spacetx#1697) - Make map/reduce APIs more intuitive (spacetx#1686) - updates roadmap to reflect 2020H1 plans - adding aws scaling vignette (spacetx#1638) - Use thresholded binarize and mask filtering in existing watershed code. (spacetx#1671) - adding spot ids to pixel results (spacetx#1687) - Implement Labeling algorithms (spacetx#1680) - Thresholded binarize conversion algorithm (spacetx#1651) - Area filter for binary masks (spacetx#1673) - Fix stain generation in watershed (spacetx#1670) - Use the new levels module. (spacetx#1669) - Linear image leveling (spacetx#1666) - add axis labels to display() (spacetx#1682) - Clip method for Richardson Lucy (spacetx#1668) - Filters for mask collections (spacetx#1659) - Provide an apply method to binary mask collections. (spacetx#1655) - adding convience method for slicing codebook data (spacetx#1626) - Fix display tests and code (spacetx#1664) - Additional builders for BinaryMaskCollection (spacetx#1637) - Methods for uncropping binary masks. (spacetx#1647) - Improve coordinate handling code for BinaryMaskCollection and LabelImage (spacetx#1632)
Tag 0.1.9 - Create an ArrayLike type (spacetx#1649) - Verify that binary masks can be generated from empty label images (spacetx#1634) - Add a morphology package to hold BinaryMaskCollection, LabelImage, and their respective operators (spacetx#1631) - fixing travis (spacetx#1648) - Support multiple codewords for the same target (spacetx#1646) - Update data model for BinaryMaskCollection (spacetx#1628) - Test for Codebook.to_json / open_json (spacetx#1645) - Simplify Dockerfile (spacetx#1642) - Switch to version exclusion for scikit-image workaround (spacetx#1629) - Clean up binary mask (spacetx#1622) - adding an extras feild to SpotFindingResults (spacetx#1615) - deleting Decode and Detect modules in lieu of spot finding refactor (spacetx#1598) - Fix install issues (spacetx#1641) - Upgrade to slicedimage 4.1.0 (spacetx#1639) - Update vocabulary for LabelImage I/O operations. (spacetx#1630) - Add a label image data type (spacetx#1619) - Remove deprecated code (spacetx#1621) - fixing bug with codebook.to_json (spacetx#1625) - Don't fill a new ImageStack with NaN (spacetx#1609) - Rename SegmenationMaskCollection to BinaryMaskCollection (spacetx#1611) - Remove hack to force anonymous memory mapping on osx (spacetx#1618)
Tag 0.1.8 - Logging improvements (spacetx#1617) - Make regionprops available per mask (spacetx#1610) - Don't use mypy 0.740 (spacetx#1616) - changing test code to use new spot finding modules (spacetx#1597) - refactoring allen smFish with new spot finding (spacetx#1593) - clean up max projection (spacetx#1379) - Use masked fill to produce labeled images (spacetx#1582) - Replace most instances of starfish.image.Filter.Reduce with imagestack.reduce (spacetx#1548) - implementing starMap spot finding refactor (spacetx#1592) - Add __slots__ to classes that subclass xr.DataArray (spacetx#1607) - Convert SegmentationMaskCollection to a dict-like object (spacetx#1579) - Test case for multiprocessing + imagestack (spacetx#1589) - Masked fill method (spacetx#1581) - Add map/reduce methods to ImageStack (spacetx#1539) - Unify FunctionSource in Map and Reduce (spacetx#1540)
Tag 0.1.7 - ISS refactored with new spot finding path (spacetx#1518) - Fix bugs in per-round-max-decoder (spacetx#1602) - Fix dimension ordering on Codebook and IntensityTable (spacetx#1600) - provanance logging refactor and support for SpotFindingResults (spacetx#1517) - napari 0.2.0 release (spacetx#1599) - starfish.display: unpin napari version, add tests, view masks separately (spacetx#1570) - adding coordinate support to SpotFindingResults (spacetx#1516) - adding new SpotFindingResults data structure and new packages (spacetx#1515)
Tag 0.1.6 - Switch to python multithreading (spacetx#1544) - Don't waste memory/compute in preserve_float_range (spacetx#1545) - Get rid of shared state for LocalMaxPeakFinder (spacetx#1541) - map filter (spacetx#1520) - funcs passed to apply and transform can use positional arguments (spacetx#1519) - import SegmentationMaskCollection in main starfish (spacetx#1527) - Enable Windows builds on master (spacetx#1538) - Throw a warning when the data size is unusual. (spacetx#1525)
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