CHANGELOG.md

0.3.0 - 2024-10-05

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

0.2.2 - 2021-04-29

• 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)

0.2.1 - 2020-06-08

• 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)

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)

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)

0.1.9 - 2019-11-18

• 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)

0.1.8 - 2019-10-18

• 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)

0.1.7 - 2019-10-09

• 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)

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)

0.1.5 - 2019-08-12

• 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)

0.1.4 - 2019-07-16

• Update in-place experiment writing to use the new WriterContract API in slicedimage 4.0.0 (#1447)
• data set formatter with fixed filenames (#1421)

0.1.3 - 2019-07-09

• 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)

0.1.2 - 2019-06-19

• Refactor reduce to take an optional module and only a function name. (#1386)
• Codify the expectation that in-place experiment construction does not rely on TileFetcher data (#1389)
• Warn and return empty SpotAttributes when PixelDecoding finds 0 spots (#1400)
• updating data.merfish link to full dataset (#1406)
• Rename tile_coordinates to tile_identifier (#1401)
• Support for irregular images in the builder (#1382)
• Fix how we structure the run notebook rules. (#1384)
• updated loading data docs and added image of napari viewer (#1387)
• Format complete ISS experiment and expose in starfish.data (#1316)
• Add concatenate method for ExpressionMatrix (#1381)
• Add TransformsList repr (#1380)
• Fix 3d smFISH notebook as well. (#1385)
• Add custom clip Filter classes (#1376)
• Fix smFISH notebook. (#1383)
• Add Filter.Reduce (general dimension reduction for ImageStack) (#1342)
• Handle denormalized numbers when normalizing intensities/codebooks (#1371)
• TileFetcher formats complete 496 fov MERFISH dataset (#1341)
• Refactor fov.getImage() to fov.getImages() (#1346)
• Add the ability to write labeled experiments (#1374)
• Add inplace TileFetcher module back to public builder API (#1375)
• Always create Z coordinates, even on 4D datasets. (#1358)
• Create an all-purpose ImageStack factory (#1348)
• Remove physical_coordinate_calculator.py (#1352)
• ImageStack parsers should provide coordinates as an array (#1351)
• bump to slicedimage 3.1.1 (#1343)
• Creating a standard starfish.wdl that can be run with any recipe file (#1364)

0.1.1 - 2019-05-16

• [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)

0.1.0 - 2019-04-23

• public/private separation (#1244)
• Recipe and recipe execution (#1192)
• 3d smFISH notebook (#1238)
• SeqFISH notebook (#1239)
• Adding windows install instructions (#1227)
• vectorize labeling spot lookups (#1215)
• vectorize imagestack -> intensity_table coordinate transfer (#1212)
• Fix the restoration of non-indexed axes. (#1189)
• Allow for intensity tables with labeled axes (#1181)
• ImageStack select on Physical Coordinates (#1147)
• fixing Clip.SCALE_BY_IMAGE (#1193)
• Update BaristaSeq text, fix LinearUnmixing (#1188)
• Update STARmap notebook for SpaceJam (#1199)
• replace label images with segmentation masks (#1135)
• BaristaSeq + Plot tools update (#1171)
• Intensity Table Concat Processing (#1118)

0.0.36 - 2019-04-10

• 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)

0.0.35 - 2019-04-03

• Transfer physical Coords to Expression Matrix (#965)
• Support for hierarchical directory structures for experiments. (#1126)
• Pipeline Components: LearnTransform and ApplyTransform (#1083)
• Restructure the relationship between PipelineComponent and AlgorithmBase (#1095)

0.0.34 - 2019-03-21

• 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)

0.0.33 - 2019.02.14

• Last release without a changelog!