scverse/spatialdata: v0.0.12

Add multichannel blobs sample data (by @melonora

scverse/spatialdata: v0.0.11

Improved aggregation APIs

scverse/napari-spatialdata: v0.2.8

<h2>[0.2.8] - 2023-10-30</h2> <h3>Added</h3> <ul> <li>Global parameters POINT_THRESHOLD and POLYGON_THRESHOLD added to allow users to adjust these parameters.</li> </ul> <h3>Fixed</h3> <ul> <li>Updated dependencies</li> <li>Updated installation instructions since napari conda-forge no longer installs Qt backend. @psobolewskiPhD</li> <li>Allow for viewing SpatialData object with no annotations. @aeisenbarth</li> </ul&gt

scverse/napari-spatialdata: v0.3.0

<h3>Added</h3> <ul> <li>New APIs for changing coordinate systems #169</li> <li>New APIs for adding single elements #170</li> <li>Improved code to link new layers to layers with a <code>SpatialData</code> object #173</li> </ul> <h3>Fixed</h3> <ul> <li>Enabled saving annotations #168</li> <li>Added safeguard when table is None #177 @aeisenbarth</li> <li>Fix plotting annotations when changing element #175</li> <li>Fixed installation requirements #185 @goanpeca</li> </ul&gt

scverse/spatialdata-io: v0.0.9

<h3>Fixed</h3> <ul> <li>(Xenium) bug when converting feature_name #81, from @fbnrst</li> <li>(Visium) visium() supports file counts without dataset_id #91</li> </ul&gt

scverse/napari-spatialdata: v0.3.1

<h3>fixed</h3> <ul> <li>removed npe (napari plugin engine) dependency</li> </ul&gt

scverse/spatialdata: v0.0.15

<h3>Fixed</h3> <ul> <li>Fixed data type error with SpatialImage and MultiscaleSpatialImage</li> </ul&gt

scverse/spatialdata: v0.0.13

Added polygon_query() support for images #358 Fixed Fix missing c_coords argument in blobs multiscale #342 Replaced hardcoded string with instance_key #34

scverse/spatialdata: v0.0.14

Added Major get_extent() function to compute bounding box of the data Minor testing against pre-release packages Fixed Fixed bug with get_values(): ignoring background channel in label

SpatialData : an open and universal data framework for spatial omics

Spatially resolved omics technologies are transforming our understanding of biological tissues. However, the handling of uni- and multimodal spatial omics datasets remains a challenge owing to large data volumes, heterogeneity of data types and the lack of flexible, spatially aware data structures. Here we introduce SpatialData, a framework that establishes a unified and extensible multiplatform file-format, lazy representation of larger-than-memory data, transformations and alignment to common coordinate systems. SpatialData facilitates spatial annotations and cross-modal aggregation and analysis, the utility of which is illustrated in the context of multiple vignettes, including integrative analysis on a multimodal Xenium and Visium breast cancer study. SpatialData is a user-friendly computational framework for exploring, analyzing, annotating, aligning and storing spatial omics data that can seamlessly handle large multimodal datasets