Bipolar-v2.0.0

This release of the toolbox is focused on DataViewer and therefore on processing imaging data from low to medium throughput experiments. The old umIToolbox app, which handled file and project management for high-throughput experiments, is not part of this release. An alternative is planned for a later version.

📖 Documentation

What's new compared with Astrocyte

• DataViewer rebuilt from scratch. It is now the single application. The ROI Manager is part of it, with event interaction, pipeline execution and a Management menu.
• Self-describing .dat files. Each .dat now carries a 512-byte header with its shape, class and frame rate. The associated per-file .mat metadata files are no longer written.
• .umt files for processed data. In Astrocyte, analysis results were saved as plain .mat files. They are now saved as .umt files, a .mat file with its own extension and a defined, versioned structure. They carry their own metadata, so you can still open them directly in MATLAB. They will later feed dedicated tools for group comparison and statistical analysis.
• Projects (optional). Project > Subject > Session projects and image references, managed with the new Project Manager.
• Rig Manager. Rigs, optical library and dual-camera coregistration. Each Save Folder records its rig in UMITRigLedger.json (Folder rig).
• Pipeline Manager. A non-modal window with a parameter panel and a zoomable graph. Unchanged steps are skipped on re-run, and DataViewer has a batch pipeline mode.
• Renamed analysis functions. The run_ prefix was dropped (for example SpeckleMapping, HemoCompute).
• Corrected analysis bugs. Fixes include the X/Y swap on drawn import ROIs, the visual sign map masking, and zero-filled columns in HemoCompute.

Removed or not yet integrated

• The old umIToolbox app and the tools it launched (Data Grouping, Data Selector, plotting tools, StatsManager). A replacement for high-throughput file and project management is planned for a later version.
• The Protocol > Subject > Acquisition model.
• Several analysis functions (trim_movie, SPCM, alignFrames, normalizeCOND, and others). Group statistics has no replacement in this release.
• mergeRecordings is still included, but it is not integrated into the GUIs yet. In Astrocyte it was used mainly by the umIToolbox app. GUI integration is planned for a later version.

⚠️ Compatibility with data from previous versions

Bipolar v1.0.0 is only partially compatible with data generated in previous versions of the toolbox. You may have to redo some work.

• Raw/processed .dat files: usually still readable, including those that have per-file metadata .mat files.
• Astrocyte result .mat files: This version of Bipolar writes .umt instead, and the planned group-analysis tools will target .umt. Re-run the analysis to get .umt outputs.
• Other processed data and ROI files: may not work, because several result files and ROI files changed format (ROI files). Re-run the affected analyses and re-create the ROIs.
• Numeric results can differ: NaN handling, event/baseline handling, retinotopy, response features and hemodynamics were revised. Don't pool data outputs from different versions without checking them first.
• Saved pipelines: pipelines that use renamed or removed functions must be rebuilt.
• Folders imported earlier: folders imported with an older release need to be bound to a rig before hemodynamic computation (DataViewer: Management > Rig > Folder Rig, see Folder rig).

Keep your current version installed for analyses on existing data that you can't redo.