Large-image

Features

- Add default_encoding and default_projection config values ([1846](../../pull/1846), [1854](../../pull/1854))

Improvements

- Apply background color information from openslide sources ([1819](../../pull/1819))
- Memoize a check for DICOM series UID ([1827](../../pull/1827))
- Speed up finding adjacent DICOM files in girder ([1829](../../pull/1829), [1836](../../pull/1836))
- Ipyleaflet region indicator ([1815](../../pull/1815))
- Add minWidth and minHeight to zarr sink ([1831](../../pull/1831))
- Reformat metadata for non-uniform axis values ([1832](../../pull/1832))
- Reorder zarr axes in read mode ([1833](../../pull/1833))
- Allow selecting inverted histogram ranges in the UI ([1839](../../pull/1839))
- Jupyter: Increase default zoom on small images ([1843](../../pull/1843), [1852](../../pull/1852))
- Debounce histogram requests in the frame selector ([1844](../../pull/1844))
- Better parse ImageJ channel names ([1857](../../pull/1857))

Changes

- Require a minimum version of Pillow to avoid a CVE ([1828](../../pull/1828))

Bug Fixes

- Zarr Sink: Allow X and Y to have length 1 ([1837](../../pull/1837))
- Ask zarr to use zero rather than empty arrays ([1840](../../pull/1840))
- Harden the ometiff reader against erroneous axis values ([1847](../../pull/1847))
- The annotation geojson output was erroneously requiring a closed flag ([1859](../../pull/1859))

Improvements

- Improve how we use vips to read lower tile levels ([1794](../../pull/1794))
- Be more specific in casting when converting images via vips ([1795](../../pull/1795))
- Improve how ometiff internal metadata is exposed ([1806](../../pull/1806))
- Show histogram auto range calculated values ([1803](../../pull/1803))
- Test reading from lower tile levels in bioformats ([1810](../../pull/1810))

Bug Fixes

- Fix an issue with lazy tiles that have non power of two scaling ([1797](../../pull/1797))
- Use zarr.empty not np.empty when creating large zarr sinks ([1801](../../pull/1801))
- Fix zarr sink addTile when no samples axis is specified ([1805](../../pull/1805))
- Fix zarr sink adding an xy axis ([1807](../../pull/1807))
- Fix adding axes one at a time with zarr sink ([1808](../../pull/1808))

Features

- Add utility functions for converting between frame and axes ([1778](../../pull/1778))
- Jupyter frame selector ([1738](../../pull/1738), [1792](../../pull/1792), [1793](../../pull/1793))

Improvements

- Better report if rasterized vector files are geospatial ([1769](../../pull/1769))
- Provide some latitude in vips multiframe detection ([1770](../../pull/1770))
- Don't read multiplane ndpi files with openslide ([1772](../../pull/1772))
- Harden sources based on more fuzz testing ([1774](../../pull/1774))
- Default to not caching source in notebooks ([1776](../../pull/1776))
- Automatically set the JUPYTER_PROXY value ([1781](../../pull/1781))
- Add a general channelNames property to tile sources ([1783](../../pull/1783))
- Speed up compositing styles ([1784](../../pull/1784))
- Better repr of large_image classes ([1787](../../pull/1787))
- Better detect multiframe images in PIL ([1791](../../pull/1791))

Changes

- Allow umap-learn for graphing in girder annotations in python 3.13 ([1780](../../pull/1780))
- List a few more known extensions for different sources ([1790](../../pull/1790))

Bug Fixes

- Fix scaling tiles from stripped tiffs in some instances ([1773](../../pull/1773))
- Updated jupyter support for ipyleaflet ([1775](../../pull/1775))

Features

- Allow gdal to read and rasterize vector formats ([1763](../../pull/1763))

Improvements

- Harden the geojson annotation parser ([1743](../../pull/1743))
- Add more color palettes ([1746](../../pull/1746))
- Improve the list of extensions the bioformats source reports ([1748](../../pull/1748))
- Improve handling of ome-tiff files generated by bioformats ([1750](../../pull/1750))
- Read jp2k compressed associated images in tiff files ([1754](../../pull/1754))
- Improve writing to zarr sinks from multiple processes ([1713](../../pull/1713))
- Slightly faster GDAL validateCOG ([1761](../../pull/1761))
- Improve clearing caches ([1766](../../pull/1766))
- Harden many of the source reads ([1768](../../pull/1768))

Changes

- Suppress a warning about nd2 files that we can't do anything about ([1749](../../pull/1749))
- Zero empty areas in tile frames ([1755](../../pull/1755))
- Don't include cache libraries in [common] deployments ([1758](../../pull/1758))
- Specify empty_dir=yes when constructing vsicurl parameters ([1760](../../pull/1760))
- Update how some associated images are read in tiff files ([1763](../../pull/1763))
- Pin zarr < 3 ([1767](../../pull/1767))

Bug Fixes

- Harden the tile cache between python versions and numpy versions ([1751](../../pull/1751))
- Cast histogram ranges to floats ([1762](../../pull/1762))

Improvements

- When using the multisource to composite multiple images with alpha channels, use nearest neighbor for upper tiles ([1736](../../pull/1736))
- Read magnification values from DICOM when reading them via bioformats ([1741](../../pull/1741))

Changes

- Adjust how compositing is done on styled images by adjusting the expected full alpha value ([1735](../../pull/1735))

Bug Fixes

- Fix a bug handling pure uint8 data introduced in 1725 ([1734](../../pull/1734))