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Version History

CaliAli 1.4.8 Release Notes — March 2026

  • Easier processing for large datasets: Added batch downsampling support so long recordings can be processed in smaller chunks with lower memory risk.
  • Smoother scripted workflows: Improved handling of user-provided file lists so automated pipelines are less likely to open unexpected file-selection windows.
  • More reliable alignment outputs: Added stronger frame-integrity checks to catch incomplete or corrupted outputs earlier.
  • Better recovery behavior: Some partially written intermediate files are now detected and regenerated automatically.
  • CNMF-E startup improvements: Fixed a demo-data crash and improved input handling when launching extraction.
  • Quality-of-life updates: Added add_paths() helper to quickly include CaliAli folders in the MATLAB path.

CaliAli 1.4.6 Release Notes — November 2025

  • Parallel processing restored: A bug in 1.4.5 forced single-core execution; multi-core execution is back.
  • Memory sizing fixes: Batch sizing during CNMF iterations is now more stable.
  • Patch-size migration fix: For 1.4.5 option files, run CaliAli_update_parameters('patch_dims',[64,64]) and resave before relaunching jobs.
  • Full 16-bit storage: Video data are now stored as uint16 to preserve dynamic range (with larger file size).

CaliAli 1.4.5 Release Notes — October 2025

  • Auto sizing improvements: batch_sz accepts 'auto', and gSig defaults to 5 / spatial_ds.
  • Clearer logs: Status and warnings were improved with colored command-window output.
  • Preprocessing updates: Improved non-negativity handling and optional median denoising.
  • Robust alignment/file handling: Better handling of frame-size changes, chunk frame counts, and natural sorting.
  • Initialization preview: Added Check_initialization_parameters.
  • Additional bug fixes: Motion-correction input handling and parameter-selection stability improvements.
  • Enhanced demo: Updated Demo_pipeline.mlx with synthetic full-resolution examples.

CaliAli 1.4 Release Notes — September 26th 2025

  • Automatic session chunking: batch_sz splits oversized sessions across motion correction, alignment, and projection steps. See Processing Large Sessions.
  • Batch helpers: Added create_batch_list() and pre_allocate_outputs().
  • Memory/resilience tweaks: Improved fallback behavior and lighter spatial updates.
  • Interactive cropping: Added CaliAli_crop().
  • Projection refinements: Better chunk aggregation consistency.
  • Migration note: batch_sz = 0 preserves legacy behavior.

Older Versions (Archived)

CaliAli 1.3 — August 2025
  • Introduced low-memory mode for large sessions.
  • Simplified BV detection pipeline.
  • Added interactive parameter-selection demos and app updates.
CaliAli 1.2.2 / 1.2.1 / 1.2 — February to May 2025
  • Split alignment flags into translation and non-rigid controls.
  • Added force_non_negative_tolerance.
  • Major parameter/pipeline modularization in v1.2.
  • Added documentation for split-session processing and multiple bug fixes.
CaliAli 1.0.1 / 1.0 / 1.0-beta — 2023 to 2024
  • First stable releases and core pipeline stabilization.
  • Documentation expansion and GUI fixes.
  • Initial publication release aligned with the BioRxiv preprint.