Optinist

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.

Improvements
Features
- Add button to create new workflow with empty workflow https://github.com/arayabrain/barebone-studio/pull/109
- Visualize is available soon after reproduce https://github.com/arayabrain/barebone-studio/pull/112
- RUN target would be highlighted https://github.com/arayabrain/barebone-studio/pull/120
- You can try tutorial sample from GUI https://github.com/arayabrain/barebone-studio/pull/182

GUI
- node id is displayed on workflow node https://github.com/arayabrain/barebone-studio/pull/108
- Improve RECORD table view https://github.com/arayabrain/barebone-studio/pull/119 https://github.com/arayabrain/barebone-studio/pull/110
- Show workspace id in multiuser mode https://github.com/arayabrain/barebone-studio/pull/123
- Improve dialogs https://github.com/arayabrain/barebone-studio/pull/124 https://github.com/arayabrain/barebone-studio/pull/189 https://github.com/arayabrain/barebone-studio/pull/211
- Improve parameter fields https://github.com/arayabrain/barebone-studio/pull/209 https://github.com/arayabrain/barebone-studio/pull/146
- Make adding plot for column direction easier https://github.com/arayabrain/barebone-studio/pull/210
- Improve drag select area https://github.com/arayabrain/barebone-studio/pull/219

Bug Fix
- Fix output movies cannot be played over index 10 https://github.com/arayabrain/barebone-studio/pull/243
- Fix browser console errors and warnings https://github.com/arayabrain/barebone-studio/pull/133 https://github.com/arayabrain/barebone-studio/pull/206
- Fix issues on multiple workflow run https://github.com/arayabrain/barebone-studio/pull/127

Enhance environments, developer support
- Update node version to LTS 20 https://github.com/arayabrain/barebone-studio/pull/79
- Use poetry to manage python modules https://github.com/arayabrain/barebone-studio/pull/132
- Add codespell https://github.com/arayabrain/barebone-studio/pull/137
- Update CI https://github.com/arayabrain/barebone-studio/pull/97
- Add FE linter and formatter https://github.com/arayabrain/barebone-studio/pull/114
- Update .env settings https://github.com/arayabrain/barebone-studio/pull/125
- Make standalone mode settings easier https://github.com/arayabrain/barebone-studio/pull/159

What's Changed
Improvements
* rename download file identifier https://github.com/oist/optinist/pull/570
* add plot metadata https://github.com/oist/optinist/pull/573

Bug Fix
* frontend developer mode missing env by default https://github.com/oist/optinist/pull/566
* fix visualize crash by another workflow https://github.com/oist/optinist/pull/568
* fix errors on ROI edit https://github.com/oist/optinist/pull/569 https://github.com/oist/optinist/pull/575

Update documents
* update installation guides for developer.
* update docker run command.
* add explanation for uploading folder as input.
* add explanation for switch timeseries plot's xaxis unit.
* add guide for customizing to show plot metadata.
* fix saving_dir path names.

**Full Changelog**: https://github.com/oist/optinist/compare/v1.0.0...v1.0.1

What's Changed
Breaking Changes
- **IMPORTANT**
- **Due to following updates, previous versions' optinist files cannot be loaded.**
- **Please set new empty directory as `OPTINIST_DIR` to use OptiNiSt >=1.0.0**

- Save branched pipeline results into single nwb file.
- Each algorithm node is identified by id, and separated in nwb file.
- Update cell index initial values
- Detected cells' id was started from 1, but now start from 0.
- Specify frame rate, fs in NWB settings
- imaging_plane.imaging_rate in NWB settings are used as frame rate in any algorithms.
- Switch unit for frame/time in TimeSeries plots
- You can switch x range unit between frame / time in TimeSeries plots like fluorescence.
- Fetch last run session
- If you reload the workflow window unintentionally, last executed workflow will be restored.
- Share workflow config
- In your device, you can reproduce your workflow. To reproduce same workflow in other devices, you can download workflow config file and share it. It can be imported in workflow tab and create same workflow.
- Add multiuser mode
- You can host OptiNiSt in your own server.
- In multiuser mode you can
- use OptiNiSt with authenticated users
- manage users
- share workflow results within your hosted environment
- See details in Host for Multiuser section in docs.


Add new analysis method
- CaImAn CNMF-E
- DPCA in optinist demention reduction

Add new plot types
- Pie Chart
- Histogram
- Polar Plot
- Line Graph

Note: Currently, there are no algorithms to show these type of plots.



**Full Changelog**: https://github.com/oist/optinist/compare/v0.4.0...v1.0.0

- Bug Fix
- 490
- 498
- Update documents
- 493