23.03.0

• Docker Image scalableminds/webknossos:23.03.0 🐳
  Run it via export DOCKER_TAG=="23.03.0" && ./start-docker.sh.
• Changelog
• Commits

Highlights

• Remote datasets can now also be streamed from Google Cloud Storage URIs (gs://). #6775
• Remote volume datasets in the neuroglancer precomputed format can now be viewed in WEBKNOSSOS. #6716
• Added new mesh-related menu items to the context menu when a mesh is hovered in the 3d viewport. #6813

Added

• If an annotation that others are allowed to edit is opened, it will now be automatically locked. This prevents conflicts when multiple users try to edit it at the same time. #6819
• Highlight 'organization owner' in Admin>User page. [#6832](#6832
• Added OME-TIFF export for bounding boxes. #6838 #6874
• Added functions to get and set segment colors to the frontend API (api.data.{getSegmentColor,setSegmentColor}). #6853

Changed

• Limit paid team sharing features to respective organization plans. #6767
• Rewrite the database tools in tools/postgres to JavaScript and adding support for non-default Postgres username-password combinations. #6803
• Added owner name to organization page. #6811
• Remove multiline <TextArea> support from . #6839
• Improved the performance of the dataset table in the dashboard. #6834
• Updated the styling and background of login, password reset/change and sign up pages. #6844
• Replaced date handling and formatting library momentjs with dayjs. #6849

Fixed

• Fixed saving allowed teams in dataset settings. #6817
• Fixed log streaming in Voxelytics workflow reports. #6828 #6831
• Fixed some layouting issues with line breaks in segment list/dataset info tab. #6799
• Fixed basic auth for exploring remote http datasets. #6866
• Fixed the layouting in the connectome tab. #6864
• Fixed that the quick-select and floodfill tool didn't update the segment list. #6867
• Fixed deprecation warnings for antd' component in Navbar. #6860
• Fixed that trying to reload a precomputed mesh via context menu could crash webKnossos. #6875

Removed

• Removed the old Datasets tab in favor of the Dataset Folders tab. #6834

23.02.1

• Docker Image scalableminds/webknossos:23.02.1 🐳
  Run it via export DOCKER_TAG=="23.02.1" && ./start-docker.sh.
• Changelog
• Commits

Fixed

• Fixed a benign error message which briefly appeared after logging in. #6810

23.02.0

• Docker Image scalableminds/webknossos:23.02.0 🐳
  Run it via export DOCKER_TAG=="23.02.0" && ./start-docker.sh.
• Changelog
• Commits

Highlights

• Changed branding of WEBKNOSSOS including a new logo, new primary colors, and UPPERCASE name. #6739
• Precomputed meshes can now be loaded even when a mapping is active (HDF5 or an editable mapping produced by the proofreading tool). The precomputed mesh has to be computed without a mapping for this to work. #6569

Added

• The target folder of a dataset can now be specified during upload. Also, clicking "Add Dataset" from an active folder will upload the dataset to that folder by default. #6704
• The storage used by an organization’s datasets can now be measured. #6685

Changed

• For remote datasets that require authentication, credentials are no longer stored in the respective JSON. #6646
• Improved performance of opening a dataset or annotation. #6711
• Redesigned organization page to include more infos on organization users, storage, webKnossos plan and provided opportunities to upgrade. #6602
• Improves performance for ingesting Voxelytics reporting data. #6732
• Implements statistics from combined workflow runs in the Voxelytics reporting. #6732
• Limit paid task/project management features to respective organization plans. 6767
• The dataset list route GET api/datasets no longer respects the isEditable filter. #6759
• Upgrade linter to Rome v11.0.0. #6785

Fixed

• Fixed node selection and context menu for node ids greater than 130813. #6724 and #6731
• Fixed the validation of some neuroglancer URLs during import. #6722
• Fixed a bug where deleting a dataset would fail if its representation on disk was already missing. #6720
• Fixed a bug where a user with multiple organizations could not log in anymore after one of their organization accounts got deactivated. #6719
• Fixed rare crash in new Datasets tab in dashboard. #6750 and #6753
• Fixed toggling "Render missing data black" when being logged out. #6772
• Fixed incorrect loading of precomputed meshes from mesh files that were computed for a specific mapping. #6771
• Fixed a bug where remote datasets without authentication could not be explored. #6764
• Fixed deprecation warnings for antd props. #6765
• Fixed a bug where direct task assignment to a single user would fail. #6777
• Fixed a bug where the dataset folders view would not list public datasets if the requesting user could not also access the dataset for other reasons, like being admin. #6759
• Fixed a bug where zarr-streamed datasets would produce (very rare) rendering errors. #6782
• Fixed a bug where publicly shared annotations were not viewable by users without an account. #6784
• Fixed proofreading when mag 1 doesn't exist for segmentation layer #6795
• Fixed that the proofreading tool allowed to split/merge with segment 0 which led to an inconsistent state. #6793

Breaking Changes

• Changes the storage backend for Voxelytics logging from Elasticsearch to Loki. #6770
• The dataset list route GET api/datasets no longer respects the isEditable filter. #6759

23.01.0

• Docker Image scalableminds/webknossos:23.01.0 🐳
  Run it via export DOCKER_TAG=="23.01.0" && ./start-docker.sh.
• Changelog
• Commits

Highlights

• Added a new datasets tab to the dashboard which supports managing datasets in folders. Folders can be organized hierarchically and datasets can be moved into these folders. Selecting a dataset will show dataset details in a sidebar. #6591
• webKnossos is now able to recover from a lost webGL context. #6663
• Major performance improvements for brushing in coarse magnifications. #6708

Added

• Added sign in via OIDC. #6534
• Added the option to search a specific folder in the new datasets tab. #6677
• The new datasets tab in the dashboard allows multi-selection of datasets so that multiple datasets can be moved to a folder at once. As in typical file explorers, CTRL + left click adds individual datasets to the current selection. Shift + left click selects a range of datasets. #6683

Changed

• Bulk task creation now needs the taskTypeId, the task type summary will no longer be accepted. #6640
• Error handling and reporting is more robust now. #6700
• The Quick-Select settings are opened (and closed) automatically when labeling with the preview mode. That way, bulk labelings with preview mode don't require constantly opening the settings manually. #6706

Fixed

• Fixed import of N5 datasets. #6668
• Fixed a bug where it was possible to create invalid an state by deleting teams that are referenced elsewhere. 6664
• Miscellaneous fixes for the new folder UI. #6674
• Fixed import of remote datasets with multiple layers and differing resolution pyramid. #6670
• Fixed broken Get-new-Task button in task dashboard. #6677
• Fixed access of remote datasets using the Amazon S3 protocol #6679
• Fixed a bug in line measurement that would lead to an infinite loop. #6689
• Fixed a bug where malformed json files could lead to uncaught exceptions.#6691
• Fixed rare crash in publications page. #6700
• Respect the config value mail.smtp.auth (used to be ignored, always using true) #6692

Removed

Breaking Changes

22.12.0

• Docker Image scalableminds/webknossos:22.12.0 🐳
  Run it via export DOCKER_TAG=="22.12.0" && ./start-docker.sh.
• Changelog
• Commits

Highlights

• Added a new Quick-Select tool for volume annotation. This tools allows to draw a rectangle over a segment to annotate it automatically. The tool operates on the intensity data of the visible color layer and automatically fills out the segment starting from the center of the rectangle. Next to the tool, there is a settings button which allows to enable a preview mode and to tweak some other parameters. If the preview is enabled, the parameters can be fine-tuned while the preview updates instantly. #6542
• The scale bar is now included in screenshots of the viewports made using the Q shortcut or the "Screenshot" menu entry. If the scale bar should not be included, disable it using "Settings - Viewport Options - Show Scalebars". #6644

Added

• The largest segment id for a segmentation layer can be computed automatically from the dataset settings page. #6415
• Button for switching organizations for Voxelytics workflows. #6572
• Added ability to shuffle / set colors for a whole tree group. #6586
• Annotation layers can now be removed. #6593
• When adding remote Zarr datasets with multiple channels, channels are converted into layers. #6609
• When adding a remote OME-NGFF dataset with labels, these are added as segmentation layers. #6638
• When creating an annotation from the dataset view, a previously selected mapping of the segmentation layer is now automatically selected in the volume annotation layer fallback segmentation as well. #6647

Changed

• The log viewer in the Voxelytics workflow reporting now uses a virtualized list. #6579
• Node positions are always handled as integers. They have always been persisted as integers by the server, anyway, but the session in which a node was created handled the position as floating point in earlier versions. #6589
• Jobs can no longer be started on datastores without workers. #6595
• When downloading volume annotations with volume data skipped, the nml volume tag is now included anyway (but has no location attribute in this case). #6566
• Re-phrased some backend (error) messages to improve clarity and provide helping hints. #6616
• The layer visibility is now encoded in the sharing link. The user opening the link will see the same layers that were visible when copying the link. #6634
• Voxelytics workflows can now be viewed by anyone with the link who is in the right organization. #6622
• Improve performance for handling of volume annotation data (saving/undo/redo). #6652
• When importing an annotation into an existing annotation, webKnossos ensures that bounding boxes are not duplicated in case they exist in the current and imported annotation. #6648
• Reworked the proofreading mode so that agglomerate skeletons are no longer needed (nor automatically loaded). Instead, segments can be selected by left-clicking onto them, indicated by a small white cross. To merge or split agglomerates, then either use the shortcuts Shift + Leftclick/Ctrl + Leftclick or use the context menu. #6625

Fixed

• Fixed a bug in the dataset import view, where the layer name text field would lose focus after each key press. #6615
• Fixed importing NGFF Zarr datasets with non-scale transforms. #6621
• Fixed a regression in NGFF Zarr import for datasets with no channel axis. #6636
• Fixed broken creation of tasks using base NMLs. #6634
• Fixed that the precomputation of meshes didn't take the active mapping into account. #6651
• Fixed false-positive warning about an outdated annotation version. #6656

22.11.3

Fixed

• Fixed broken creation of tasks using base NMLs. #6634

22.11.2

• Docker Image scalableminds/webknossos:22.11.2 🐳
  Run it via export DOCKER_TAG=="22.11.2" && ./start-docker.sh.
• Changelog
• Commits

Changed

• When merging annotations, bounding boxes are no longer duplicated. #6576

Fixed

• Fixed importing a dataset from disk. #6615

22.11.1

• Docker Image scalableminds/webknossos:22.11.1 🐳
  Run it via export DOCKER_TAG=="22.11.1" && ./start-docker.sh.
• Changelog
• Commits

Added

• Turned successful dataset conversions into a clickable link. #6583

Fixed

• Fixed a rare crash in newer Firefox versions. #6561
• Fixed the positions of precomputed meshes when using a v3 mesh file. #6588

22.11.0

• Docker Image scalableminds/webknossos:22.11.0 🐳
  Run it via export DOCKER_TAG=="22.11.0" && ./start-docker.sh.
• Changelog
• Commits

Highlights

• Remote n5 datasets can now also be explored and added. #6520
• Tasks can now be assigned to individual users directly. #6551
• Support for a new mesh file format which allows up to billions of meshes. #6491

Added

• The task creation page now links to creation pages for task types, projects etc., for a smoother task administration experience. #6513
• Improved performance for applying agglomerate mappings on segmentation data. #6532
• Added backspace as an additional keyboard shortcut for deleting the active node. #6554
• When reloading a layer, because the underlying data has changed, the histogram will also be reloaded and reflect the changes. #6537
• Enable "What's New" update information for all instances. #6563
• Add context-menu option to delete skeleton root group. #6553
• Added remaining task time estimation (ETA) for Voxelytics tasks in workflow reporting. #6564
• Added a help button to the UI to send questions and feedbacks to the dev team. #6560

Changed

• Creating tasks in bulk now also supports referencing task types by their summary instead of id. #6486
• Navbar changes: Move dropdown menu into separate Menu button. Removed toggle-button (cog icon)for left-hand side bar from navbar. #6558
• Upgraded Typescript to v4.8 #6567

Fixed

• Fixed a bug where some file requests replied with error 400 instead of 404, confusing some zarr clients. #6515
• Fixed URL for private Zarr streaming links to volume annotations. #6515
• Fixed a bug where the transform of a new mesh file wasn't taken into account for the rendering of meshes. #6552
• Fixed a rare crash when splitting/merging a large skeleton. #6557
• Fixed a bug where some features were unavailable for annotations for datasets of foreign organizations. #6548

22.10.0

• Docker Image scalableminds/webknossos:22.10.0 🐳
  Run it via export DOCKER_TAG=="22.10.0" && ./start-docker.sh.
• Changelog

Highlights

• Added a context menu option to extract the shortest path between two nodes as a new tree. Select the source node and open the context menu by right-clicking on another node in the same tree. #6423
• Add setting for gamma correction for color and grayscale layers in the left sidebar. #6439
• Added a context menu option to separate an agglomerate skeleton using Min-Cut. Activate the Proofreading tool, select the source node and open the context menu by right-clicking on the target node which you would like to separate through Min-Cut. #6361
• The color of a segments can now be changed in the segments tab. Rightclick a segment in the list and select "Change Color" to open a color picker. #6372
• Sharing links are shortened by default. Within the sharing modal, this shortening behavior can be disabled. #6461
• The largestSegmentId is no longer a required property for segmentation layers. It is still recommended to set the property, since the generation of new segment IDs is blocked during volume annotation. However, annotating with manually set IDs is still possible. This change simplifies the import of datasets into webKnossos. #6414

Added

• Zarr-based remote dataset import now also works for public AWS S3 endpoints with no credentials. #6421
• Added a "clear" button to reset skeletons/meshes after successful mergers/split. #6459
• The proofreading tool now supports merging and splitting (via min-cut) agglomerates by rightclicking a segment (and not a node). Note that there still has to be an active node so that both partners of the operation are defined. #6464
• Added workflow reporting and logging features for Voxelytics into webKnossos. If activated, the workflows can be accessed from the Administration > Voxelytics menu item. #6416 #6460
• Added possibility to read N5 datasets. #6466
• Added "shift + w" shortcut to cycle backwards through annotation tools. #6493

Changed

• Selecting a node with the proofreading tool won't have any side effects anymore. Previous versions could load additional agglomerate skeletons in certain scenarios which could be confusing. #6477
• Removed optional "resolution" parameter from /datasets/:organizationName/:dataSetName/layers/:dataLayerName/data route. Use mag instead. #6479
• Changed how volumes containing no data are stored. Now the selection of magnifications is correctly exported and imported. #6481
• The "Restore Older Version" list is now paginated which improves performance for in case many versions exist. #6483

Fixed

• Fixed sharing button for users who are currently visiting a dataset or annotation which was shared with them. #6438
• Fixed the duplicate function for annotations with an editable mapping (a.k.a. supervoxel proofreading) layer. #6446
• Fixed isosurface loading for volume annotations with mappings. #6458
• Fixed importing of remote datastore (e.g., zarr) when datastore is set up separately. #6462
• Fixed a crash which could happen when using the "Automatically clip histogram" feature in certain scenarios. #6433
• Fixed loading agglomeate skeletons for agglomerate ids larger than 2^31. #6472
• Fixed bug which could lead to conflict-warnings even though there weren't any. #6477
• Fixed that one could not change the color of a segment or tree in Firefox. #6488
• Fixed validation of layer selection when trying to start globalization of floodfills. #6497
• Fixed filtering for public datasets in dataset table. #6496