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Release Notes

24.5

Platform

  • It is now possible to specify a compute resources tier as a parameter for tasks in analysis tables, allowing for custom control over the CPU, memory, and GPU resources allocated
  • Resource usage metrics can be viewed along with the logs after task completion and relevant errors are displayed if tasks failed due to a resource issue (eg. out of memory)

  • The user who started a task is now displayed alongside other task information on analysis tables

  • Analysis table layout changes were made to support these newly added columns/parameters and to improve usability on smaller displays, including:

    • The task information columns are no longer pinned to the right or collapsed into a group by default, and are instead displayed after the results columns - a button to scroll to these columns was added to the menu bar and they have been added to the “Jump to” column dropdown
    • The task status is now displayed as an icon in the actions column with additional information on hover
    • The tool version column is no longer pinned and is displayed at the start of the table after the task ID

  • Non-empty analysis tables now can be deleted (executed tasks contained in the table will be automatically deleted with it)

  • Datasets can be deleted (a choice is prompted to delete the dataset’s files or move them to the project)

  • Projects can be sorted in the projects dashboard by recent activity and total size
  • Users will receive a notification when a project is shared with them at the individual or organization level
  • Project admins can now specify whether external viewers can download or copy projects when sharing a project
  • Projects can be copied without including files and tasks in order to replicate only the project structure (datasets, columns, analysis tables)
  • Copying projects is disabled/cannot be initiated if the organization does not have enough active and archived space left to contain it (instead of having to wait until the copy process ends to be notified)
  • The All Tasks view in projects now displays system tasks like file processing and DANDI exports that do not appear on an analysis table to allow for total accounting of compute resources

Fixes

  • E-focus metadata shows correctly for all files
  • Fixed ‘.unknown’ suffix added when downloading files without a file type
  • Improved performance for bulk creating analysis table rows
  • Notifications sidebar stays open when marking notifications as read at smaller window widths

  • Compute credit total on analysis table responds to all changes (deleting, task completion) without refreshing

  • Fixed error while unarchiving series files

  • The compute credits total displayed on analysis tables no longer includes credits for deleted rows (credit consumed by deleted rows remain visible in the All Tasks table)
  • Analysis table layout does not break at small window sizes
  • Cloning large projects consumes less memory resources
  • Fixed an issue with file deletion for organizations with an expired contract

24.4

Platform

  • Organization admins can now view all organization projects from the organization usage page, instead of the home page. This new table view of all projects enables admins to easily inventory their IDEAS subscription usage, as well as modify project access when needed.
  • Organization admins can edit the organization name by clicking the gear icon > Edit Organization Name from the organization home page.
  • All users can now filter and sort projects from either the user or organization home page.
    • Filter and sorting state will now be remembered when navigating back/forward from these pages.
    • Users can filter projects to any role/access level.
  • Users can pin projects to the top of their user or organization homepage to easily access frequently visited projects.
  • Users can cancel a file upload in progress.
  • Users can cancel an analysis task in progress.
  • For uploaded files where 1) no file type is detected or 2) metadata and preview generation failed, users can select which file type. For supported types (e.g., Bruker 2P movies), this will trigger metadata extraction and preview generation.

Analysis Tools

  • nVision Animal Tracking Model and Extract Tracking Data From nVision Movie tools now support multiple simultaneous zone occupancies (i.e., in the case of overlapping zones).
  • All tools that output experiment annotation files now include all column names in the output file metadata, which can be directly used as inputs in downstream tools.
  • Peri-Event Analysis Workflow tool now only analyzes 'accepted' cells when present in cell set. Otherwise, if all cells have no status or are 'undecided', all cells are included.

Bug Fixes

  • Organization admins will see their current access/role on projects instead of just “Admin”.
  • Unexecuted analysis table rows will now correctly identify themselves as unable to start if inputs are archived.
  • Fixed an issue where navigating to the analysis table via a file’s “generated by” link would not work when already on an analysis table page.
  • Fixed an issue where adding rows to an analysis table from a dataset would not populate optional input parameters.

24.3

Platform

  • Projects can now be duplicated (cloned) within and across organizations
  • Organization admins can now manage their organization's members, including the ability to invite new users to join their organization
    • New users who have been invited to join an organization can self-register an IDEAS account
    • Users can be removed from organizations by organization admins
  • Analysis tables now support multiple versions on an analysis on a single table instead of requiring an entirely new table to be created with each version.
    • Compatible versions that do not change the input data or parameters of an analysis will be available on the same table alongside existing versions, and users can see and choose what version a task will be run with.
    • New versions that change the inputs or parameters can be added as a new tab to existing tables
  • Users can now manually specify the file type of any uploaded file that was not automatically identified
    • Users can also view the processing log for files that failed to extract previews or generate metadata to understand why the failure occurred
  • Added several new notifications to be displayed for events like being invited to an organization, completion of project cloning, changes to user role in an organization, and failure to process an uploaded file.
  • A new browser to select analyses is now available when creating new analysis tables, organizing analyses by toolkit and allowing users to name the new table before creating it
  • Added support for processing timestamp events h5 files
  • Added support for ZIP files in DANDI exports

Analysis Tools

  • Add support for converting behavior videos to the NWB format
  • Improve and optimize conversion of large miniscope movies to the NWB format
  • Extend support for exporting behavior videos to DANDI along with miniscope movies, cell sets, and event sets
  • Update the crop rectangle and ROI parameters to use the new ROI editor interface in the Preprocess, Motion Correct, End-To-End CNMF-E, and End-To-End PCA-ICA tools
  • Rename Export Movie to MP4 tool to Convert Inscopix Movie to MP4

Bug Fixes

  • Fixed an issue where files added to an analysis table from the dataset view would not always immediately appear
  • Fixed an issue where the autofill button would get cut off when too many recording IDs displayed in the recordings column in analysis tables

24.2

Platform

  • Add ability to share projects across accounts
  • New user and organization home pages
  • New ROI GUI to define regions of interest directly from input movies in behavior data processing tools
  • Add ability to reference file and recording metadata when populating parameters in analysis tables
  • Improved and faster project deletion

Analysis Tools

Bug Fixes

  • Remove duplicated tools from the analysis tool menu
  • Remove spaces from file names produced by the combine-and-compare tools to allow files to be downloaded
  • Fix issue associated with traces plot in the Calcium Imaging QC Report tool when processing series data

24.1

Platform

  • The file browser can now be displayed from the main project page and will display all files in the project across all datasets and analyses, including files without a dataset assignment
  • Uploaded files can be assigned/reassigned to empty cells in a dataset by clicking on the new assignment icon when hovering the cell (alternative to dragging and dropping from the file browser)
  • Styling updates to increase the amount of information that can be displayed in dataset, analysis table, and tasks views
  • Archive/unarchive/delete actions are available when viewing file details in an analysis table
  • Added expandable details to the All Tasks view to display a summary of task inputs and results
  • Added ability to search and navigate with the keyboard when selecting file inputs for analysis tables

Analysis Tools

Bug Fixes

  • Deleting a file that was in the process of uploading will immediately allow the next queued file to start uploading
  • Analysis results are displayed dataset file browser when the current dataset filter is applied
  • File detail view will automatically close itself if the file it is displaying is deleted
  • Improved stability when deleting a file results in a network error
  • Fixed an issue where the file detail view would sometimes close unexpectedly
  • Fixed an issue where analysis table result attachments to dataset would sometimes reset
  • The fill handle will not attempt to populate read-only cells in analysis tables
  • Resolved an issue where tasks could get stuck in queued state
  • Fixed inverted cell set footprints previews
  • Fixed metadata extraction issue preventing processing of some nVision movies
  • Fixed preview loading issue associated with multiplexing movies

23.7

Platform

  • Tasks can now be deleted from analysis tables after execution - deleting a completed task will also delete its result files
  • The new “View All Tasks” page provides a central interface for viewing and auditing all submitted tasks within a project (including ones that have been deleted from their original analysis table)
  • A “Recording Session IDs” column has been added to the analysis table view that displays the recording(s) associated with the task and its results (automatically read from the selected input files)
  • The “Autofill from recording” action on the new recordings column will attempt to fill in a task’s input files based on a selected recording (if a single matching file can be found)
  • A new streamlined “Add Column” dialog simplifies the process of inserting uploaded data, metadata, and result columns to datasets
  • Improved the column deletion and removal process on datasets, including a new group header menu that allows you to delete any or all grouped analysis result columns in a single action.
  • The new dialog that appears will display any linked columns that will also be automatically removed
  • Deleting an uploaded data column will also delete the files assigned to it (a warning will display)
  • Projects display your level of access on the home page and project dashboard
  • Enabled range selection on dataset recordings tables
  • Data selector improved with better support for smaller screen sizes & auto-selection of options with only one choice
  • Redesigned the usage metrics dialog in the menu bar and on the Organization page

Bug Fixes

  • Fixed an issue where the download option was not displaying for individual files in a series
  • A warning will display if you try to close IDEAS while changes to a dataset are syncing
  • The input on the “Insert recording row(s)” dialog can now be cleared
  • Fixed an issue where the option to archive would incorrectly display on already-archived files
  • Fixed an issue where uploading files through clicking on a cell would occasionally fail to start the upload
  • Fixed an issue where deleting a file that is currently uploading could later cause a crash in some cases
  • fixed a bug in the Map Boris Annotations To ISXD Data tool where outputs were not visible.
  • fixed a bug in the Map Annotations To ISXD Data tool where Miniscope movies were not selectable as inputs.
  • Improvements to documentation and better generation of documentation from sources.

23.6

Platform

  • Users can directly export NWB files from IDEAS to the DANDI Archive to publicly share and store their data.
  • New permissions and sharing capabilities to allow users to share Projects with specific users in their organization and specify levels of access, including view-only, edit access, and administration.
  • IDEAS cloud computing resource monitoring has now migrated to using a new compute credits system. Users can directly see how many compute credits are consumed by each Analysis Table task.
  • Added ability to directly draw a region of interest on an image to use as input for spatially cropping miniscope movies during preprocessing.

Analysis Tools

23.5

Platform

  • Added ability to process series data in synchronization, correlation, and population activity tools
  • Added ability to process series data in calcium imaging quality control report tool
  • Added system to notify users when a new version is released
  • Added new recording identifiers system

Analysis Tools

  • New Trim Movie tool to remove frames from a miniscope movie
  • New Deconvolve Traces tool to estimate the underlying neural spikes and biosensor kinetics (e.g. GCaMP activity) from noisy calcium imaging fluorescent time-series data
  • New Detect Events tool to convert a CSV file to event timestamps that can be used in downstream analyses (e.g. Peri-Event Analysis Workflow)
  • Added new filters to the Automated Accept/Reject Cells tool to allow more granular cell filtering

Bug Fixes

  • Fixed an issue where duplicate filenames as analysis inputs weren’t staged correctly
  • Fixed calculation of project size when they contain multiple datasets
  • Fixed project size not reflected after uploads until after refresh
  • Fixed bug where detail view on a cell with multiple files would get stuck open
  • Fixed bug where dropdown menu on dataset would get stuck open
  • Fixed bug with stuck tooltips on disabled elements
  • Fixed filter cells tool document link
  • Fixed a bug where searches with some special characters would not work on file browser
  • Fixed a bug where multiple files from the same recording on the analysis table would cause a duplicated recording in the file info flyout
  • Fixed a bug where analysis results would not always show up on analysis tables until refresh
  • Fixed a crash when trying to archive a file that does not belong to a dataset

23.4

Platform

  • Projects now support multiple datasets
  • An all-new data selector for analysis inputs
  • User is prompted when a new tool version is available for an Analysis Table
  • Track and highlight the file that is currently viewed in the info fly-out
  • A global upload UI component showing currently uploading files that their status
  • Table column width modifications are persisted
  • New layout for the dataset with a bottom bar
  • Attachment of analysis results back to multiple source recordings
  • Preview files from the file browser
  • A revised projects page shows data tables and analysis tables
  • New movie previews
  • Unique identifier for Tasks on the Analysis table

New Analysis Tools

  • Synchronize Annotations to Cell Set
  • Synchronize State Annotations to Cell Set
  • Average Population Neural Activity
  • Neural Circuit Correlations
  • Combine and Compare Peri-Event Analysis Data
  • Combine and Compare Population Activity Data

Bug Fixes

  • Fixed upload issue for large files over slow and unstable internet connections when the upload process spans multiple hours.
  • Fixed dataset crashing issue due to orphan uploaded files and analysis table results from deleted analysis tables
  • Fixed duplicate metadata output from series
  • Fixed user navigation pop-up not hiding after navigating to a page
  • Fixed order of cell set data previews (footprints and traces)

23.3

Platform

  • Deployed IDEAS EU environment
  • The Uploaded Files table is now a general File Browser that includes analysis result files and displays source details (ie. user-uploaded vs. generated through an analysis)
  • Added text search and uploaded/analysis result filters to File Browser
  • Simplified the menu bar in the Dataset view and added shortcuts to view Notes, Analyses, and File sidebars
  • Enabled renaming files from the File Browser view
  • Enabled downloading files from the File Browser view
  • Enabled reordering and ungrouping of analysis result columns in dataset
  • Added linked analysis table details to analysis result column headers
  • Enabled viewing of input file details and previews in analysis tables
  • Added optional descriptions to saved versions of datasets, made name optional when saving a version
  • Added descriptive titles to application pages that can be seen in browser tabs and history
  • Analysis results have more descriptive names (naming convention follows IDPS)
  • New cell set data preview
  • New CSV events data preview
  • Added ISXD image previews
  • Can view the current End-User License Agreement from the Settings page
  • Improved platform security

Analysis Tools

  • Added standalone Detect Events tool
  • Added support for series to the cell filtering tool

Bug Fixes

  • Fixed an issue where analysis table dropdown menus would get stuck open
  • Fixed an issue that could cause long-running uploads (eg. very large files) to fail on upload completion
  • Fixed upload issue associated with some .imu files
  • Fixed an issue with date formatting in the File Browser
  • Fixed an issue where a “zoom in” cursor would be displayed when hovering already-expanded preview images (now displays “zoom out”)
  • Fixed an issue where the selected cell would not stay highlighted when viewing File information in the dataset view

23.2

Platform

  • Added end user level agreement (EULA)
  • Improved uploaded files view with additional information, sorting, and bulk actions
  • File browser can be expanded or viewed in full screen
  • Added channel and focus metadata fields to movies, cell sets, and event files
  • Series can be ungrouped back into individual files
  • Enabled column reordering in dataset recordings table
  • Enabled column pinning in dataset recordings table
  • Improved dataset recordings table column menu interface
  • Allow renaming of metadata columns in the dataset recordings table
  • Added detail view that shows the column and metadata field that metadata columns are linking to
  • Enabled export/download of dataset recordings table and analysis tables as .csv
  • Improved display of input files and file selector in analysis tables
  • Improved display of deleted or archived files that have been selected as inputs in analysis tables

New Analysis Tools

  • De-interleave Movie (Calcium Imaging Processing Toolkit)
  • Added the ability to de-interleave multiplane and dual-color movies to the Preprocess tool
  • Added support for multiplane and dual-color movies to the cell identification workflows (End-to-End CNMF-E, End-to-End PCA-ICA)
  • Added tool
  • Added Downsample tool

Bug Fixes

  • Fixed displaying storage sizes
  • Fixed tracking of CPU usage and download resource usage and units
  • Analysis tables that have been hidden will not show up in the analysis table results column selector as an option
  • Fixed occasional crash when editing with analysis table cells
  • Fixed analysis table displaying a loading indicator when new recordings or files were selected

23.1

Platform

  • Added support for archiving and unarchiving files
  • Added support for creating movie, cell set, and events series
  • Added file information and source to detailed file view
  • Added support for viewing Task logs directly
  • Improved tooltips and inline documentation, particularly for file upload, display, and interactions
  • Improved resilience to network outages, uploads in progress will pause during network outages and automatically resume when possible
  • Added support for deleting files from storage without removing them from history or metadata (historical deletion is still an option as well)
  • Projects can be deleted
  • Performance improvements and enhanced error reporting
  • Add notes to Projects and Datasets

New Calcium Imaging Processing Analysis Tools

Bug Fixes

  • Fixed an issue where the project description input would clear its value
  • Parameters no longer overflow off screen when in the “jump to parameter” view
  • Calcium Imaging QC Report result can now be viewed without downloading