NEWS

VoltRon 0.3.1

Both x and y coordinates of SIFT/ORB landmarks are now checked after alignment with registerSpatialData.
Intersection, Bhattacharyya, and newly added Structural Similarity index measure are now calculated for chunks/tiles of image pairs. The "local SSIM" per each tile are provided to report on the local alignment quality. Aggregate values of these three measures are also used to report on the global alignment score.

registerSpatialData now allows registering assays with no images. In case of either one of the assays, do not have images, assays can be registered with only the manual approach.
The Shiny interface for registerSpatialData now reports on the accuracy of the alignment using multiple metrics such as Intersection, Bhattacharyya and Matte's Mutual Information.
An image-free alignment tutorial has been added where DBIT-Seq and a QuPath processed mIF experiment are aligned using manually selected landmarks.
transferData now allows integrating single cell data object (Seurat or SingleCellExperiment) for transfering features (e.g. gene expression) or metadata features (e.g. cell types, annotations).
Now importImageData and importQuPathIF functions only work with segments already converted to a list by the user, or the generateSegments function whose argument is an sf object.
The formAssay function now accepts only segments without the user manually generating coordinates (or centroids).
The name argument in functions like vrImages, vrCoordinates and vrSegments is replaced with spatial which is the name of the spatial coordinate system of the assay, spatial object.
The formImage function is replaced with formSpatial to avoid confusion.

Fix anndataR conversion by removing var_names and obs_names arguments and fix other faulty arguments

Added instructions to install VoltRon from R-universe.
Added instructions to install SimpleITK binaries from BIMSBbioinfo/SimpleITKRInstaller.

Non-rigid fine alignment with SimpleITK combined with landmark-based manual coarse alignment. Now, registerSpatialData function will let users to select BSpline (SimpleITK) method for non-rigid alignment when Non-Rigid methods selected.

Non-rigid fine alignment (with OpenCV coarse alignment) using SimpleITK

https://bioinformatics.mdc-berlin.de/VoltRon/registration.html#Non-Rigid_Alignment
Added 'channels' arguement to ImportImageData to parse only requested channels from OME-TIFF files.

https://bioinformatics.mdc-berlin.de/VoltRon/importingdata.html#OME-TIFF
Multi-omic clustering with multiple feature sets and tutorials (Xenium + mIF) upon registration

https://bioinformatics.mdc-berlin.de/VoltRon/multiomic.html#Xenium_+_IF_Tonsil_Data
Added importQuPathIF function to generate QuPath processed images and import spatial proteomics assays as a VoltRon objects

https://bioinformatics.mdc-berlin.de/VoltRon/importingdata.html#Multiplex_IF_(QuPath){.uri}
Building spatial neighborhood graphs and proximity analysis across multiple entities (e.g. molecules vs cells)

https://bioinformatics.mdc-berlin.de/VoltRon/multiomic.html#Hot_Spot_Analysis