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1. kuwisdelu commented on Dec 19, 2024

   

   kuwisdelu

   on Dec 19, 2024

   Last edited by kuwisdelu

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   Spring 2025

   Cardinal 3.10 (Bioconductor 3.21 - expected April)

   This will be our 10th anniversary edition! We can be ambitious. Among other new features, this should finally be the release where we introduce a GUI.

   • Graphical user interface
     • Based on shiny
     • Visualization only (for now)
     • Maybe preview pre-processing?
     • iMSI()? MSIView()? msiView()?
   • Ion mobility (experimental)
     • Support for timsTOF via TIMSCONVERT to imzML
     • Add readTIMSData() function
     • Read mobility arrays with cvParam "MS:1003006"
     • Load data as TIMSImagingExperiment
     • Add peakProcess() method for TIMSImagingExperiment
     • Pre-release on Github in February/March?
   • Co-registration (experimental)
     • Native support for simple linear and affine transformations
     • Add coregister method based on matter::warp2_trans()
     • Aim to be good enough for visualization, but not necessarily annotation
     • More advanced methods coming later in CardinalNN

   CardinalNN 0.99 (under development)

   This will be our companion package for any neural network-based methods requiring Python.

   • Prototype R package
   • Define Basilisk virtual environments
   • Methods for serializing core objects to Python
     • Need to figure out how to map to Python classes
     • May need to pull data into memory for matter -> numpy.ndarray
     • Eventually we'll want native matter objects in Python
   • Bindings for msireg?
     • Need to coordinate with Sai
   • Bindings for mzclustering?
     • Khoury Research Apprenticeship project

   👍React with 👍1Reacted by AMAwatermelon
2. kuwisdelu

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   on Dec 19, 2024
3. kuwisdelu

   pinned this issue on Dec 19, 2024
4. kuwisdelu commented on Jan 30, 2026

   

   kuwisdelu

   on Jan 30, 2026

   Last edited by kuwisdelu

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   None of the above happened because US politics overwhelmed the author.

   Let's try again.

   Spring 2026

   Cardinal 3.14 (Bioconductor 3.23 - expected April)

   This update will be focused on usability and cleaning up the public API.

   • Refactor core classes
     • Decouple MSImagingArrays and MSImagingExperiment
     • Use MSImagingArrays for processing spectra
     • Use MSImagingExperiment for downstream analysis
   • Refactor spectral processing
     • Harmonize processing function implementations
     • Refactor process()
     • Refactor peakProcess()
     • Remove unnecessary generic functions
   • Refactor results storage
   • Refactor imzML import/export
   • Refactor pixels() and features()

   CardinalStats (under development)

   Statistical learning methods will be moved to a new package.

   • Prototype CardinalStats package
   • Implement nearest neighbor methods (BiocNeighbors)
   • Implement dimension reduction methods (BiocSingular)
   • Implement clustering methods (bluster)