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starfish: unified pipelines for image-based transcriptomics
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0.2.2
3 years ago
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
3 years ago
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
4 years ago
[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
4 years ago
[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
4 years ago
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
4 years ago
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
4 years ago
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
4 years ago
[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
4 years ago
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)
0.1.4
4 years ago
Update in-place experiment writing to use the new WriterContract API in slicedimage 4.0.0 (#1447)
data set formatter with fixed filenames (#1421)
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