- Updating CHANGELOG.md for release 0.3.1
- Adding support to Python 3.12 (#2027)
- Numpy 1.26 update to support Python 3.12 (#2025)
- fixing blob radius calculation in 2d (#2023)
- Release 0.3.0 (#2021)
- 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)
- 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)
- 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)
- 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)
- Update the documentation for data formatters (#1476)
- add ability to convert segmentation masks to a label image
- If in_place=True, we should return None (#1473)
- downgrade pyparsing (#1467)
- fixes unicode in issue template (#1464)
- Adds issue templates (#1460)
- Updating requirements. (#1461)
- Bump to slicedimage 4.0.1 (#1458)
- on-demand loading of data. (#1456)
- Get rid of the check-requirements cron job. (#1448)
- Fixing travis build (#1457)
- removing duplicate file (#1455)
- Remove Cli (#1444)
- Instantiate the multiprocessing pool using `with` (#1436)
- Slight optimization of pixel decoding (#1412)
- [easy] point starfish.data.osmFISH() to new dataset (#1425)
- [easy] Warn about the deprecation of the MaxProject filter (#1390)
- [Easy] Fixing spot detection for labeled axes (#1347)
- Schema versioning (#1278)
- Add a missing parameter to wrapper for trackpy local max peak finder (#1300)
- Fix physical coordinate calculator (#1350)
- Fix spot detection for labeled data. (#1349)
- Adding back ability to crop on fov.get_image() (#1329)
- RFC: Base calling filter for in situ sequencing (#1281)
- Preserve subpixel offsets from spot detection (#1330)
- Update strict requirements (#1142)
- High level goal: detect spots should accept imagestacks and not numpy arrays. (#1143)
- Remove cropping from PixelSpotDetector, (#1120)
- Add LocalSearchBlobDetector to support BaristaSeq, SeqFISH, STARmap (#1074)
- Indirect File click types (#1124)
- Move the registration tests next to their sources. (#1134)
- Test to verify that inplace experiment construction works. (#1131)
- Additional support code for building experiments in-place. (#1127)
- Adding ability to pass aligned group to Imagestack.from_path_or_url (#1069)
- Add Decoded Spot Table (#1087)
- Enable appending to existing napari viewer in display() (#1093)
- Change tile shape to a dict by default (#1072)
- Add ElementWiseMult Filter Pipeline Component (#983)
- Add linear unmixing pipeline component (#1056)
- Spiritual Bag of Images Refactor: Part 1 (#986)
- Add to provenance log (#968)