Optinist

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

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`.

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](https://github.com/oist/optinist/blob/main/docs/specifications/algorithm_nodes.md#roi-and-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.

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)

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.

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.