Changelog • SpatialFeatureExperiment

Version 1.6.1 (05/09/2024)

readRDS converts old style SpatRasterImage to the new style
readSelectTx and addSelectTx functions to read transcript spots from a few select genes from the parquet output of formatTxSpots or add them to an SFE object
Added formatTxTech and addTxTech functions, basically thin wrappers of formatTxSpots and addTxSpots with presets for Vizgen, Xenium, and CosMX

Changed defaults from sample_id = NULL to sample_id = 1L when dealing with 1 sample or “all” when dealing with multiple samples
dim method for BioFormatsImage that doesn’t load the image into memory
Deal with univariate spatial results in featureData in cbind and changeSampleID
Fixed super embarrassing bug in cbind that fails when combining more than 2 SFE objects
Updated readXenium for XOA v2
Updated BioFormatsImage to store affine transform info rather than converting to EBImage after transform
Speed up affine transformation of sf geometries with sfheaders
Coercion from Seurat to SFE
SpatRasterImage and EBImage directly inherit from SpatRaster and Image respectively so the user no longer needs to call imgRaster every time they plots or operates on the image, which I find really annoying.
Changed name EBImage to ExtImage to reduce confusion
Bug fixes on image affine transformation
Exporting some util functions: aggBboxes, getPixelSize, and imageIDs
Read select genes as rowGeometry and add to existing rowGeometry without erasing existing genes in the same rowGeometry

Added readXenium (for XOA v1)
Added BioFormatsImage and EBImage classes to deal with Xenium OME-TIFF
Conversion between SpatRasterImage, BioFormatsImage, and EBImage
Overhaul of geometry operation functions for images and SFE objects for the new image classes, including bbox, crop, and affine transforms
Don’t throw error when there are no rows or columns left after [ subsetting
cbind for multiple samples that have rowGeometry
Rewrote df2df with the much faster sfheaders, deprecating the less efficient BPPARAM argument

Refactored to remove “missing” methods for geometries, graphs, and local results.
Changed defaults from sample_id = NULL to sample_id = “all” unless only one sample can be specified.

Fixed bug when Visium graph is not added when filtered matrix from only one sample is read with read10xVisiumSFE.
Changed the way pixels are converted to microns in Visium. Old way: use top left corner of Visium spot array to compute spacing between spots, doesn’t work for filtered data when there’re singleton spots. New way: Use median row/col indices, more robust when there’re singletons. When spacing is used for the conversion, spot size is found to vary across datasets.
Added saveRDS method for SFE objects, so SpatRaster images are wrapped before saving and unwrapped on the fly when they’re requested.
Fixed bug when the wrong bounding boxes are used to crop images when SFE object is subsetted and there’re multiple samples.

Read images as SpatRaster, in read10xVisiumSFE
read10xVisiumSFE can also convert full resolution image pixels to microns based on Visium spot spacing
read10xVisiumSFE no longer transposes output from read10xVisium so the spots would match the image by default, and to be consistent with SpatialExperiment
Read standard Vizgen MERFISH output with readVizgen
SpatRasterImage class inheriting from VirtualSpatialImage for SpatialExperiment compatibility
Methods of addImg, mirrorImg, and transposeImg for SpatRasterImage and SFE
Mirror and transpose SFE objects, operating on both geometries and images
Images are cropped when the SFE object is cropped
Images are also shifted when removeEmptySpace is called

Store SFE package version in object and added SFE method of updateObject to pave way for a potential reimplementation of spatialGraphs.

Use BiocNeighbors for k nearest neighbors and distance based neighbors, preserving distance info to avoid slow step to refind distances with sf as done in spdep.
Added swap_rownames argument in localResult(s) getters so gene symbols from any rowData column can be used to get local results stored under Ensembl IDs.

Correctly move the geometries when there are multiple samples
Use translate = FALSE when using localResult setter for geometries
More helpful error messages when geometries, localResult, or spatial graphs are absent