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Changelog

semla 1.4.0

2025-09-08

Changes

  • Increased versions of semla’s dependencies:
    • Seurat v5 or above
    • ggplot2 v3.5.2 or above
  • GetSpatialNetwork() can compute the network on either array or pixel spot coordinates.
  • Cleaned up warnings that come inside testing

semla 1.3.2

2025-07-4

Changes

  • Bug fix for UpdateSeuratForSemla() when dealing with VisiumV2 data. VisiumV2 assays can contain both VisiumHD and Visium data. With Visium data, regular array coordinates cannot be returned, which could cause issues when running specific plotting methods downstream. Thus, we recommend using semla’s ReadVisiumData() in order to read the data into memory.

semla 1.3.1

2025-03-19

Changes

  • If the spot barcode IDs are missing a “-N” (e.g. “-1”) suffix (like is standard in Visium data), it will be added to the IDs when running ReadVisiumData(). This ensures that multiple samples can be added and merged properly without conflicts with unique barcode identities.

  • Minor edits to the backend code for plotting functions

semla 1.3.0

2025-02-26

Added

  • Functionalities added for creating a spatial multimodal object using the new function CreateMultiModalObject(). This new function takes two objects, which have had their pixel coordinates aligned to each other beforehand, and joins them into a new object where the spatial points from the second “mapping” modality are mapped and aggregated onto the first “reference” modality. The data in the two modalities are stored as separate assays in the new object.

Changes

  • Changed the appearance of the color scalebar in MapFeatures() and MapMultipleFeatures() so that the ticks and outline colors are black and have the same linewidth.
  • MapFeaturesSummary() now has a default option set for the subplot_type argument (default = “violin”).

Bug fixes

  • Minor fixes in function documentations

semla 1.2.1

2025-01-24

Bug fixes

  • Fixed an issue with the RadialDistance() function to make it possible to pass additional arguments, such as maxDist and nNeighbors. Related to Issue #36

Added

  • The UpdateSeuratForSemla function now accepts VisiumV2 assays. Related to Issues #41 and #40

semla 1.2.0

2024-09-27

Bug fixes

  • Dealt with an issue in MapFeatures and MapLabels if the specified column contains NA values and when using SeuratObject v.5.

  • When running RegionNeighbors and specifying a column in which labels contain any blank spaces, the function will abort and a message will be provided. (#20)

Added

  • Compatibility with parquet file format, used in Visium HD, when loading coordinate files using the LoadSpatialCoordinates function (used in ReadVisiumData).
  • New arguments, shape and spot_side, within the MapFeatures, MapLabels, MapFeaturesSummary, MapLabelsSummary, and MapMultipleFeatures functions to allow for square pixel plotting, particularly useful when working with Visium HD data.
  • A new vignette to demonstrate how to work with Visium HD data has also been added to the website.
  • Added a new argument, image_use, to the UpdateSeuratFromSemla function, allowing the user to decide if they want to put the raw or the transformed image in the new object (#33).
  • Optional alternative to compute p-values when calculating spatial autocorrelation scores using CorSpatialFeatures. The p-values are computed using the Student t Distribution, and adjusted p-values are calculated using the Benjamini & Hochberg (BH, or FDR) method. (#22)

semla 1.1.6

2023-09-19

Bug fixes

  • Fixed bug in RunLocalG when store_in_metadata = FALSE and no alternative hypothesis is provided.
  • Fixed bug in TileImage when using multiple threads on linux.

Changes

  • Modified behaviour of mode = "heatmap" in PlotFeatureLoadings to make sure that features are ordered by their highest dimensionality reduction value.
  • Updated NNMF vignette with a new data set.
  • Changed deprecated ggplot2 function arguments in AnglePlot and MapFeaturesSummary.
  • Changed example Seurat object to contain basic array coordinates.

Added

  • Option to set launch.browser in FeatureViewer. For instance, users can se launch.browser = getOption("viewer") in FeatureViewer to launch the app in the RStudio viewer window.
  • CreateStaffliObject now accepts basic array coordinates to be stored in meta_data slot. These coordinates are defined on the capture array grid of a 10x Genomics Visium slide and do not match the H&E images.

semla 1.1.5

2023-09-06

Bug fixes

  • Added check for non-finite values when visualizing numeric data in FeatureViewer to avoid crash
  • Fixed bug in FeatureViewer when a slot other than ‘data’ is selected

semla 1.1.4

2023-09-04

Bug fixes

  • Fixed bug in LoadScaleFactors
  • Fixed bug in FeatureViewer when handling data sets with spots located outside the H&E image

Changes

  • Improved function documentation

Added

  • Added support for conversion of Seurat objects with Slide-seq data in UpdateSeuratForSemla
  • Added option to color background and titles in ImagePlot
  • Added support for Visium + IF data in LoadAndMergeMatrices and ReadVisiumData
  • Added renv.lock file for installing semla and its dependencies with renv

Website

  • Updated image alignment vignette
  • Updated Staffli objects article
  • Added cell type deconvolution benchmark article
  • Added Visium + IF data vignette
  • Added example to digital unrolling vignette

semla 1.1.0

2023-08-14

Added

  • Added helper function for Staffli objects:
    • GetScaleFactors to fetch tibble with scale factor related information
  • GetImages to fetch images
  • GetImageInfo to fetch tibble with image related information
  • ReplaceImagePaths to validate and update image paths
  • Added UpdateSeuratForSemla to make Seurat objects with VisiumV1 data compatible with semla
  • Added LoadAnnotationCSV to load annotations exported from Loupe Browser

Changes

  • Improved verbosity
  • Reduced size of example data
  • Updated function documentation
  • Updated function examples
  • Added option to load images from URL instead of local path (LoadImages and ReplaceImagePaths)
  • Added option to use multiple cores for ExportDataForViewer
  • Fixed bug in RadialDistance when no spots are available after removing singletons
  • Fixed bug in MergeSTData when merging two or more objects containing multiple tissue sections
  • Fixed bug in MapMultipleFeatures when NA values are present
  • Updated data loaders for increased compatibility with CytAssist data. Minor bug fixes for edge cases when spots are located outside of the H&E image
  • Fixed bug in LoadAndMergeMatrices when loading data from a data folder output by Space Ranger
  • Changed output of AdjustTissueCoordinates which now returns unadjusted y-axis values

semla 1.0.0

2023-03-24

We are excited to announce the first release of our R package, semla.

The package is designed to process, analyze and visualize Spatially Resolved Transcriptomics (SRT) data.

Key features of this release include:

  • Interactive data visualization and annotation with the FeatureViewer web app
  • Spatially aware analysis methods: RegionNeighbors, RadialDistance, CorSpatialFeatures, RunLocalG, RunLabelAssortativityTest, RunNeighborhoodEnrichmentTest, CutSpatialNetwork
  • Visualization methods: MapFeatures, MapLabels
  • Image processing: MaskImages, RigidTransformImages, RunAlignment
  • Cell type mapping: RunNNLS

We would like to express our gratitude to Javier Morlanes and Marcos Machado who contributed to this release. We appreciate your feedback, suggestions, and bug reports.

We invite users to download and install the development version of the package from our GitHub repo and explore the features and functionality. Please feel free to provide feedback and suggestions for future improvements.

Thank you for your support and we look forward to continuing to enhance and improve this package.

Sincerely,

Ludvig Larsson and Lovisa Franzén