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

22.09.0

• Docker Image scalableminds/webknossos:22.09.0 🐳
  Run it via export DOCKER_TAG=="22.09.0" && ./start-docker.sh.
• Changelog

Highlights

• Added an "extrude segment" feature which is similar to the old "copy from previous slice" feature. The segment interpolation and the new segment extrusion feature are both available via the toolbar (see the dropdown icon which was added to the old interpolation button). #6370
• The owner of an annotation can allow other users, who may see the annotation, to also edit it. Note that parallel writes are not supported and would lead to conflicts. #6236
• Added support for ad-hoc meshing for volume annotation layers with fallback segmentations. #6369
• Added support for 64-bit segmentations (uint64). Note that the actual support only covers IDs up to 2^53 - 1 (matches the JavaScript number type). Also note that JSON mappings are only compatible with segment ids that only use the lower 32 bits. #6317
• WebKnossos now remembers the tool that was active in between disabling and enabling the segmentation layer. #6362
• The Add Dataset view now hosts an Add Zarr Dataset tab to explore, configure and import remote Zarr datasets. #6335
• Added a UI to manage Zarr links for an annotation so that the annotation can be streamed to third-party tools. This change also includes new backend API routes for using the (private) zarr links to annotations as well as creating them. #6367

Added

• Segmentation layers which were not previously editable now show an (un)lock icon button which shortcuts to the Add Volume Layer modal with the layer being preselected. #6330
• The NML file in volume annotation download now includes segment metadata like names and anchor positions. #6347
• Added new backend API route for requesting all publications. Those publications can now have also attached annotations. #6315
• Added a "duplicate" button for annotations. #6386
• Added new filter options for the dataset list api at api/datasets: organizationName: String, onlyMyOrganization: Boolean, uploaderId: String #6377

Changed

• webKnossos uses WebGL 2 instead of WebGL 1 now. In case your browser/hardware does not support this, webKnossos will alert you and you need to upgrade your system. #6350
• The sharing modal now automatically saves changes of the sharing options. #6314
• The Layers tab now displays an Add Skeleton Annotation Layer button with which volume-only annotations can be converted to hybrid annotations. #6330
• The Zarr directory listings no longer include the current directory “.”. 6359
• The default name for volume annotation layers with fallback segmentations is now set to the name of their fallback segmentation layer, no longer “Volume”. #6373
• The “reload data” button for dataset and annotation layers is now only shown to users who have administrative permissions for the dataset (because the button clears server caches and file handles). #6380
• Requests for missing chunks in zarr datasets now return status code 404 instead of 200 with an empty response. #6381
• Dataset layer thumbnails now by default show the center of the intersection of all layer bounding boxes, so all layer thumbnails show the same region. 6411

Fixed

• Fixed a regression where the mapping activation confirmation dialog was never shown. #6346
• Fixed an error if multiple proofreading actions were performed in rapid succession. If webKnossos is busy, inputs to the viewports are disabled from now on. #6325
• Fixed that ad-hoc meshing would terminate early for large segments. #6352
• Fixed a bug where the largestSegmentId of zarr segmentation layers was not propagated from the datasource-properties.json, which broke annotating based on these layers. #6363
• Fixed a bug where uploads of wkw datasets with numerical-only layer names would fail. #6382
• Public datasets of other organizations are no longer listed during task creation. #6377
• Tightened organization isolation security for dataset uploads. #6378
• Fixed a bug with undo/redo and volume interpolation/extrusion. #6403
• Fixed a regression which caused that uint16 and uint8 segmentations could not be rendered. #6406
• Fixed a bug which prevented keyboard shortcuts from taking affect after expanding/collapsing the sidebar panels using the button icons.#6410
• Fixed a bug with the clip histogram button to prevent it from showing a loading spinner forever in some cases. #6407
• Fixed an issue whereby a warning toast would be triggered every time the 3D viewport is put into fullscreen mode. #6412

Removed

• The Annotation Type label was removed from the info tab. #6330
• Removed the possibility to load data from foreign webKnossos datastores. Use Zarr streaming instead. #6392

22.08.0

• Docker Image scalableminds/webknossos:22.08.0 🐳
  Run it via export DOCKER_TAG=="22.08.0" && ./start-docker.sh.
• Changelog

Highlights

• Merged the "Shared Annotations" tab into the "Annotations" tab in the user's dashboard. If annotations are shared with you, you can see them in your dashboard. The table can be filtered by owner if you prefer to see only your own annotations. #6230
• Add new backend API routes for working with annotations without having to provide a 'type' argument. Note that these support stored annotations (Task and Explorational), but do not work for CompoundTask/CompoundProject/CompoundTaskType annotations. For the latter, please use the original route variants with explicit type. #6285

Added

• Added a warning for invalid volume layer names. The layer names must now be unique among all layers in an annotation and must not contain url encoded special characters. #6289
• Added optional mappingName parameter to requestRawCuboid datastore route, which allows to directly apply a specified mapping in the backend. #6311
• Added option to use X-Auth-Token header instead of query parameter in every datastore and tracingstore route. #6312

Changed

• Changed the name of the volume annotation layer in tasks to be "Volume" instead of "Volume Layer". #6321
• Dataset managers are now allowed to change dataset team permissions for all teams they are a member of. #6336

Fixed

• Fixed that zooming out for datasets with very large scale was not possible until the coarsest level. #6304

22.07.0

• Docker Image scalableminds/webknossos:22.07.0 🐳
  Run it via export DOCKER_TAG=="22.07.0" && ./start-docker.sh.
• Changelog

Highlights

• Added a image data download speed indicator to the statusbar. On hover a tooltip is shown that show the total amount of downloaded shard data. #6269
• Provide a UI to download/export a dataset in view-mode. The UI explains how to access the data with the python library. #6283

Added

• Added a warning for when the resolution in the XY viewport on z=1-downsampled datasets becomes too low, explaining the problem and how to mitigate it. #6255
• Added the possibility to view and download older versions of read-only annotations. #6274
• Added a proofreading tool which can be used to edit agglomerate mappings. After activating an agglomerate mapping the proofreading tool can be selected. While the tool is active, agglomerates can be clicked to load their agglomerate skeletons. Use the context menu to delete or create edges for those agglomerate skeletons to split or merge agglomerates. The changes will immediately reflect in the segmentation and meshes. #6195

Changed

• For the api routes that return annotation info objects, the user field was renamed to owner. User still exists as an alias, but will be removed in a future release. #6250
• Slimmed the URLs for annotations by removing Explorational and Task. The old URLs are still supported, but will be redirected to the new format. #6208
• When creating a task from a base annotation, the starting position/rotation and bounding box as specified during task creation are now used and overwrite the ones from the original base annotation. #6249
• Increased maximum interpolation depth from 8 to 100. #6292

Fixed

• Fixed that bounding boxes were deletable in read-only tracings although the delete button was disabled. #6273
• Fixed that (old) sharing links with tokens did not work, because the token was removed during a redirection. #6281

22.06.1

• Docker Image scalableminds/webknossos:22.06._1 🐳
  Run it via export DOCKER_TAG=="22.06._1" && ./start-docker.sh.
• Changelog

Fixed

• Fixed that the context menu broke webKnossos when opening it in dataset-view-mode while no segmentation layer was visible. #6259
• Fixed benign error toast when viewing a public annotation without being logged in. #6271