2025/06 v2.2.1

What's Changed

• Added reference to paper to landing readthedocs page: arayabrain#863
• Update run_cluster: arayabrain#859

Full Changelog: v2.2.0...v2.2.1

2025/05 Release v2.2.0

Improvements

Documentation Updates

• Added explanation regarding Data Usage

Improvements Related to NWB

• Refactoring code for nwb process
• Removed duplicate input names and NWB templates
• Update NWB spec optinist version

Workflow Stability Improvements

• Improved stability of parallel execution when increasing node and snakemake cores
• Improved stability of parallel execution in Docker environments

Data Deletion Feature (for Multi-User Mode)

• Workspaces and Accounts are now properly deleted from both the database and local storage when removed

Bug Fixed

• Workspace Invalid API to loop when backend shut downs.
• CCA param added to wrong yaml that causing error

2025/04 Release v2.1.0

Improvements

• Enhanced NWB Spec Generation
  Improved the generation process for NWB (Neurodata Without Borders) specifications (related to saving data class).

• Expanded Deletion Options
  Added the ability to delete input data types beyond just images.

• Data Integrity in Filtering
  Data is now automatically copied before any filter is applied. This ensures both the original and filtered versions are preserved independently.

• Conda and algorithm parameters saved in NWB
  User inputs parameters and conda parameters are saved in Config folder in NWB files.

• ​Enhancing Snakemake Workflow: Performance and Concurrency Improvements

• Output Data Size
  Implemented calculation and display of user output data capacity, providing more transparency into storage usage.

• Documentation Updates
  The documentation on ReadTheDocs has been updated to reflect the latest changes in version 2.1.0.

2025/04 Release v2.0.4

Patch Notes – v2.0.4

Improvements

• Set NumPy version explicitly and update related documentation
• Add documentation note regarding lazy loading of OptiNist movie files
• Save filtered data to NWB format
• Save Conda environment YAML and Node parameters to NWB file

Bug fixes

• Fix parallel processing issues in CaImAn

2025/04 Release v2.0.3

Patch Notes – v2.0.3

Improvements

• Proxy SignIn feature
• Updated filter functionality
• Added support for Conda setup in Custom Node
• Refactored error messages for v1 yaml errors
• Refactor of the database module
• Update popup and docs for Conda environment maintenance node
• Refactored NodesLinkButton component
• Improved Log Level Filter UI/UX
• Created FAQ docs for Caiman YAML version changes

Bug fixes

• Fixed workflow hover scrolling error
• Addressed microscope node and data filter error
• removed frontend warnings

2025/03 Release v2.0.2

Patch Notes – v2.0.2

Bug Fixes

• Fixed an issue where Fluorescence could not be selected.
• Fixed a bug where ROI's Select Drag was not properly linked with Fluo.
• Resolved a problem with the change logs output directory.
• Fixed an issue where the Visualize state was not resetting as expected.

Improvements

• Added an icon next to Algo Node to easily navigate to relevant documentation.
• Adjusted the sidebar width in the Workflow interface for better usability.

Documentation

• Added a Slack community invite link to both ReadTheDocs and README.
• Added the link to the GitHub repository on ReadTheDocs.
• Introduced Docs for Debugging.

New Feature

• Added a new function: vacant_roi_function.

2025/03 Release

Documentation & User Support

• Create a tutorial on how to specify machines for the front-end and back-end.
• Enhance the FAQ and troubleshooting sections with more detailed error messages.

Workflow & Functionality Improvements

• Separate Snakemake environment setup from actual computation.
• Add a function to select cells, considering selection methods (same as ID88).
• Display descriptions for functions and parameters.
• Implement a feature to copy workflows with a new ID.
• Improve ROI-Fluo visualization: Selecting a fluorescence trace should highlight the corresponding ROI cell.
• Enable bulk display of cell numbers in the ROI screen.
• Introduce a method to prevent zombie processes (e.g., prompt users on startup whether to display past processes).
• Add a new node for roi_fluo_from_hdf5.

Bug Fixes & Technical Enhancements

• Fix bug where, after editing ROI (Commit) in s2o, the saved NWB fluorescence dimensions are reversed.
• Fix issue where drag-selecting after reproduction causes a front-end clash.
• Simplify the process of adding new modules, making it easier to check functionality after implementation.
• Upgrade Caiman to move beyond Python 3.8.
• Implement of terminal content in the front-end.

2025/01 Release

Improvements

• Improve logger and snakemake (easier debugging)
• Update settings for multiuser mode
• Major changes to backend and frontend testing scripts
• Add development mode with more information for developers
• Refactor workflow (node types)
• Improved API error handling
• Update documentation (multiuser mode, algorithm node & parameter descriptions with external links, docs improved internal links)

Bugfixes

• CaImAn dependencies & bug fix
• Suite2p updated to work with apple silicon (use miniforge)
• Bug fixes (Makefile testing, loading icon, experiment naming, authentication, edit ROI, cancelled workflow stuck indefinitely)

2024/04 Release

Improvements

• Add cnmf online option and multisession registration for memory issue on large files.
• Improve logger on code run on snakemake.

Bug Fix

• Add process to download CNN models for component evaluation after cnmf.

2024/03 Release

Improvements

• Some microscope data is available as input.
  • .isxd, .nd2, .oir
  • .nd2 and .oir requires additional setups on your environment. Please see docs for details.
• Matlab data is available as input.
• Add utilities to reproduce RoiData and FluoData from hdf5 and nwb.
• suite2p_registration returns movie so as it to be used for other algorithms.
• Add CNMF parameters.
• Add NWB setting option to save raw image into NWB's acquisition.
• Show tiff image's shape on ImageNode file selector.
• Get input files via URL.
• Restrict some feature while workflow running to prevent unintended error.
• Rename the output of suit2p_spike_deconv from FluoData to SpikingActivityData.

Bug Fix

• Cannot load 1d array data from hdf5.
• Cannot read csv with header correctly.
• CNMF fails with image larger than 4GB.
  • But still have out of memory problem. WIP to improve memory usage on large data.
• Fluo data from suite2p was not transposed in NWB.
• non-cell mask from CNMF shows background cells.
• Algorithm parameters are sorted in alphabetical order after reproduce.