KomaMRI.jl: An open-source framework for general MRI simulations with GPU acceleration

KomaMRI v0.13.0

Diff since v0.12.0

Plotting and desktop UI

• Replace PlotlyJS/WebIO with PlotlyBase, removing the legacy WebIO/JSON dependency chain and allowing Reactant to resolve to current compatible versions.
• Rebuild KomaUI() as a standalone Bonito/Electron desktop window while preserving reactive observables, file loading, simulation progress, toasts, reconstruction, and MAT export.
• Render Plotly figures through Julia's standard display system in the desktop UI, Jupyter, Pluto, and Literate/Documenter pages.
• Fix CLI shutdown when the desktop window closes and reduce first-window startup latency.

Physiological triggers

• Add CardiacSignal, NoPhysioSignal, trigger-delay resolution, and the physio simulation/plotting workflow.
• Add physiological-trigger plotting and ADC-label selection to sequence plots.
• Map nonzero NAV ADC labels to the ISMRMRD navigation-data flag.
• Add a triggered cardiac bSSFP tutorial.

Breaking changes

• Plotting functions now return PlotlyBase.Plot instead of PlotlyJS.SyncPlot; the selectable PlotlyJS/PlutoPlotly backend and plot_backend! were removed.
• The desktop UI implementation changed from Blink/Interact to Bonito/Electron.
• The minimum Julia version is now 1.10.

Merged pull requests:

• Add Pulseq-compatible SLR pulse design (#818) (@cncastillo)
• Replace PlotlyJS/Blink with PlotlyBase/Bonito and add physiological triggers (#819) (@cncastillo)
• Fix spiral base FOV and resolution scaling (#822) (@cncastillo)
• Fix desktop UI shutdown and startup (#824) (@cncastillo)

Closed issues:

• PulseDesigner submodule (#4)
• Python API (#68)
• Test files generated with Python PyPulseq (1.3) (#367)
• Move from WebIO to Bonito (#433)
• Plots not working on Google Colab (#599)
• Define minimal Python API for KomaMRI simulation (#732)
• Set up CI pipeline for Python + Julia integration (#733)
• Add Python simulation examples and validation (#735)
• Residual per-shot signal drift past ~270 s (same FP collapse as #780, two more sites) (#788)