0.3.0

What's Changed

• Update Starfish CI and dependencies by @njmei in #1963
• Update TransformsList class with to_dict() and from_dict() methods by @njmei in #1956
• Fix coords assignment in CombineAdjustFeatures.run by @sgratiy in #1965
• Revert "Fix coords assignment in CombineAdjustFeatures.run" by @berl in #1966
• Revert "Revert "Fix coords assignment in CombineAdjustFeatures.run"" by @berl in #1967
• Bump dask from 2021.9.0 to 2021.10.0 in /requirements by @dependabot in #1968
• Updated seqFISH Decoding Method: CheckAll Decoder by @nickeener in #1978
• Various Small Fixes/Improvements by @nickeener in #1985
• Add min_distance parameter to peak_local_max call by @iimog in #2008
• Scripts and dependencies updates for Python 3.8 - 3.10 by @shachafl in #2009
• Update readthedocs.yml by @berl in #2014
• Dropping support for Python 3.8 and setting Python 3.9 as minimum by @shachafl in #2018

New Contributors

• @sgratiy made their first contribution in #1965
• @nickeener made their first contribution in #1978
• @iimog made their first contribution in #2008
• @shachafl made their first contribution in #2009

Full Changelog: 0.2.2...0.3.0

Release 0.2.2

• 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

• 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

[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

[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

• 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

• 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)

Release 0.1.7

• ISS refactored with new spot finding path (#1518)
• Fix bugs in per-round-max-decoder (#1602)
• Fix dimension ordering on Codebook and IntensityTable (#1600)
• provanance logging refactor and support for SpotFindingResults (#1517)
• napari 0.2.0 release (#1599)
• starfish.display: unpin napari version, add tests, view masks separately (#1570)
• adding coordinate support to SpotFindingResults (#1516)
• adding new SpotFindingResults data structure and new packages (#1515)

Release 0.1.6

[0.1.6] - 2019-09-18

• Switch to python multithreading (#1544)
• Don't waste memory/compute in preserve_float_range (#1545)
• Get rid of shared state for LocalMaxPeakFinder (#1541)
• map filter (#1520)
• funcs passed to apply and transform can use positional arguments (#1519)
• import SegmentationMaskCollection in main starfish (#1527)
• Enable Windows builds on master (#1538)
• Throw a warning when the data size is unusual. (#1525)

Release 0.1.5

• add ability to convert segmentation masks to a label image
• If in_place=True, we should return None (#1473)
• Bump to slicedimage 4.0.1 (#1458)
• on-demand loading of data. (#1456)
• Remove Cli (#1444)