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Recent Releases of optinist

optinist - 2025/08 Release v2.2.3

What's Changed

  • Remove space at the end of filename that caused issues in windows in https://github.com/oist/optinist/pull/690
  • Added fix to solve error in using runcluster.py to run snakemake.yaml files, in particular with new nwbtemplate format in https://github.com/arayabrain/barebone-studio/pull/895

Full Changelog: https://github.com/oist/optinist/compare/v2.2.1...v2.2.3

- TypeScript
Published by milesAraya 7 months ago

optinist - 2025/08 Release v2.2.2

Added fix to solve error in using runcluster.py to run snakemake.yaml files, in particular with new nwbtemplate format Related PR: https://github.com/arayabrain/barebone-studio/pull/895

- TypeScript
Published by milesAraya 8 months ago

optinist - 2025/06 v2.2.1

What's Changed

  • Added reference to paper to landing readthedocs page: https://github.com/arayabrain/barebone-studio/pull/863/
  • Update run_cluster: https://github.com/arayabrain/barebone-studio/pull/859

Full Changelog: https://github.com/oist/optinist/compare/v2.2.0...v2.2.1

- TypeScript
Published by milesAraya 9 months ago

optinist - 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

- TypeScript
Published by tsuchiyama-araya 10 months ago

optinist - 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.

- TypeScript
Published by tsuchiyama-araya 11 months ago

optinist - 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

- TypeScript
Published by tsuchiyama-araya 12 months ago

optinist - 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

- TypeScript
Published by milesAraya 12 months ago

optinist - 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.

- TypeScript
Published by tsuchiyama-araya 12 months ago

optinist - 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 roifluofrom_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.

- TypeScript
Published by tsuchiyama-araya about 1 year ago

optinist - 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)

- TypeScript
Published by milesAraya about 1 year ago

optinist - 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.

- TypeScript
Published by ReiHashimoto almost 2 years ago

optinist - 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 suit2pspikedeconv 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.

- TypeScript
Published by ReiHashimoto almost 2 years ago

optinist - 2023/12 Release

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

- TypeScript
Published by ReiHashimoto over 2 years ago

optinist - 2023/09/28 Release

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

- TypeScript
Published by ReiHashimoto over 2 years ago

optinist - 2023/09/27 Release

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

    • imagingplane.imagingrate 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

- TypeScript
Published by ReiHashimoto over 2 years ago

optinist - 2023/05/22 Release

  • Bug Fix
    • #490
    • #498
  • Update documents
    • #493

- TypeScript
Published by ReiHashimoto almost 3 years ago

optinist - 2023/05 Release

  • New feature
    • ROI edit information is saved in NWB file
    • ROI edit is available on outputs of caimancnmf and lccdcell_detection
    • Current workflow id is displayed
  • Bug fix
    • #420
    • #429
    • #438
    • #454
    • #456
    • #459
    • #460
  • Update documents

- TypeScript
Published by ReiHashimoto almost 3 years ago

optinist - 2023/05 Release

  • New feature
    • ROI edit information is saved in NWB file
    • ROI edit is available on outputs of caimancnmf and lccdcell_detection
    • Current workflow id is displayed
  • Bug fix
    • #420
    • #429
    • #438
    • #454
    • #456
    • #459
    • #460
  • Update documents

- TypeScript
Published by ReiHashimoto almost 3 years ago

optinist - 2023/05 Release

  • New feature
    • ROI edit information is saved in NWB file
    • ROI edit is available on outputs of caimancnmf and lccdcell_detection
    • Current workflow id is displayed
  • Bug fix
    • #420
    • #429
    • #438
    • #454
    • #456
    • #459
    • #460
  • Update documents

- TypeScript
Published by ReiHashimoto almost 3 years ago

optinist - 2023/03 Release

  • New feature
    • New ROI Detect function: LCCD added
    • You can rename Workflow now.
    • ROI Edit on VISUALIZE page (currently, only suite2p works)
    • Add pipeline sample
  • Bug fix
    • https://github.com/oist/optinist/issues/377
    • https://github.com/oist/optinist/issues/378
    • https://github.com/oist/optinist/issues/379
  • Update Documents

- TypeScript
Published by emuemuJP almost 3 years ago

optinist - 2023/03 Release

  • New feature
    • New ROI Detect function: LCCD added
    • You can rename Workflow now.
    • ROI Edit on VISUALIZE page (currently, only suite2p works)
    • Add pipeline sample
  • Bug fix
    • https://github.com/oist/optinist/issues/377
    • https://github.com/oist/optinist/issues/378
    • https://github.com/oist/optinist/issues/379
  • Update Documents

- TypeScript
Published by emuemuJP almost 3 years ago

optinist -

Bug fix: install from snakemake original repository

- TypeScript
Published by ShogoAkiyama over 3 years ago

optinist -

369

- TypeScript
Published by ShogoAkiyama over 3 years ago

optinist - v0.1.0

- TypeScript
Published by ShogoAkiyama almost 4 years ago

optinist - 2022/3/23の報告会時のバージョン

- TypeScript
Published by ShogoAkiyama almost 4 years ago

optinist - 2022/2/21の報告会時のバージョン

- TypeScript
Published by ShogoAkiyama about 4 years ago