23.10.2

• Docker Image scalableminds/webknossos:23.10.2 🐳
  Run it via export DOCKER_TAG=="23.10.2" && ./start-docker.sh.
• Changelog
• Commits

Fixed

• Fixed that segment statistics were requested in the wrong resolution and without properly considering the dataset scale. #7355

23.10.1

• Docker Image scalableminds/webknossos:23.10.1 🐳
  Run it via export DOCKER_TAG=="23.10.1" && ./start-docker.sh.
• Changelog
• Commits

Fixed

• Fixed that auto-saving only took place every 5 minutes instead of every 30 seconds. #7352

23.10.0

• Docker Image scalableminds/webknossos:23.10.0 🐳
  Run it via export DOCKER_TAG=="23.10.0" && ./start-docker.sh.
• Changelog
• Commits

Highlights

• Datasets and annotations can now be more than 3-dimensional, using additional coordinates. #7136
• Volume and bounding box information is shown in segments' context menus as well as in a separate modal in the segments tab. There is also an option to export the statistics. #7249

Added

• Added disabled drag handles to volume and skeleton layers for visual consistency. These layer cannot be dragged or reordered. #7295
• Dataset thumbnails for grayscale layers can now be colored using the value in the view configuration. #7255
• OpenID Connect authorization is now compatible with Providers that send the user information in an id_token. #7294
• Segments and segment groups can be modified via the JS API. The following functions are available: registerSegment, removeSegment, updateSegment, createSegmentGroup, renameSegmentGroup, deleteSegmentGroup. #7332
• A banner underneath the navigation bar informs about current and upcoming maintenances of WEBKNOSSOS. #7284
• The AI-based quick select tool can now also be used for ND datasets. #7287

Changed

• On datasets with segment indices, ad-hoc meshing can now create non-connected meshes. #7244
• Annotating volume data uses a transaction-based mechanism now. As a result, WK is more robust against partial saves (i.e., due to a crashing tab). #7264
• Improved speed of saving volume data. #7264
• Improved progress indicator when saving volume data. #7264
• Adapted Zarr 3 implementations to recent changes in the specification (index codecs, zstd codec). #7305
• When importing datasets with additional axes (more than 3 dimensions), the axis names are now sanitized and checked for duplicates. #7308

Fixed

• Fixed that the deletion of a selected segment would crash the segments tab. #7316
• Fixed reading sharded Zarr 3 data from the local file system. #7321
• Fixed no-bucket data zipfile when downloading volume annotations. #7323
• Fixed too tight assertions when saving annotations, leading to failed save requests. #7326
• Fixed a bug when saving large amounts of skeleton annotation data at once. #7329
• Fixed a bug that prevented downloading public skeleton-only annotations by other users. #7347

23.09.0

• Docker Image scalableminds/webknossos:23.09.0 🐳
  Run it via export DOCKER_TAG=="23.09.0" && ./start-docker.sh.
• Changelog
• Commits

Highlights

• Added option to select multiple segments in the segment list in order to perform batch actions. #7242
• Added the option to change the ordering of color layers via drag and drop. This is useful when using the cover blend mode. #7188

Added

• Added configuration to require users' emails to be verified, added flow to verify emails via link. #7161
• Added a route to explore and add remote datasets via API. #7176
• Added a new button to the layer settings in view only dataset mode to save the current view configuration as the dataset's default. #7205
• If a dataset layer is transformed (using an affine matrix or a thin plate spline), it can be dynamically shown without that transform via the layers sidebar. All other layers will be transformed accordingly. #7246
• OpenID Connect authorization can now use a client secret for added security. #7263

Changed

• Small messages during annotating (e.g. “finished undo”, “applying mapping…”) are now click-through, so they do not block users from selecting tools. #7239
• When exploring remote NGFF datasets with channels, layer names and colors are automatically imported if available in the metadata. #7251
• Annotating volume data uses a transaction-based mechanism now. As a result, WK is more robust against partial saves (i.e., due to a crashing tab). #7264
• Improved speed of saving volume data. #7264
• Improved progress indicator when saving volume data. #7264
• The order of color layers can now also be manipulated in additive blend mode (see #7188). #7289
• OpenID Connect authorization now fetches the server’s public key automatically. The config keys singleSignOn.openIdConnect.publicKey and singleSignOn.openIdConnect.publicKeyAlgorithm are now unused. 7267
• When importing a remote dataset and adding another layer with a different voxel size, that layer is now scaled to match the first layer. #7213

Fixed

• Fixed that it was possible to have larger active segment ids than supported by the data type of the segmentation layer which caused the segmentation ids to overflow. #7240
• Fixed that folders could appear in the dataset search output in the dashboard. #7232
• Fixed that the edit icon for an annotation description could disappear in Firefox. #7250
• Fixed that assigning an invalid script name (e.g. with special characters) would trigger an error in the database. Now leads to a more descriptive error. #7525
• Fixed rendering error when multiple segmentation layers exist and the user switched between these. #7291

Breaking Changes

• The task and project api have changed. Make sure to update to the latest webknossos python library version when interacting with task and projects via the python library. Compare webknossos-libs#930. #7220

23.08.0

• Docker Image scalableminds/webknossos:23.08.0 🐳
  Run it via export DOCKER_TAG=="23.08.0" && ./start-docker.sh.
• Changelog
• Commits

Highlights

• Added batch actions for segment groups, such as changing the color and loading or downloading all corresponding meshes. #7164.
• Improved support for touch devices by adding floating buttons for easier navigation and layout changes. #7178
• The brush size can now be changed by selecting brush size presets. These presets are user configurable by assigning the current brush size to any of the preset buttons. Additionally the preset brush sizes can be set with keyboard shortcuts. #7101

Added

• Added a search feature for segments and segment groups. Listed segments/groups can be searched by id and name. #7175
• Added a modal to the voxelytics workflow view that lists all artifacts with their file size and inode count. This helps to identify the largest artifacts to free disk space. #7152
• Added new graphics and restyled empty dashboards. #7008
• Added warning when using WEBKNOSSOS in an outdated browser. #7165
• Re-added optional antialiasing for rendering. #7180
• Added support for transformations with thin plate splines. #7131
• WEBKNOSSOS can now read S3 remote dataset credentials from environment variables AWS_ACCESS_KEY_ID and AWS_SECRET_KEY. Those will be used, if available, when accessing remote datasets for which no explicit credentials are supplied. #7170
• Added security.txt according to RFC 9116. The content is configurable and it can be disabled. #7182
• Added routes for super-users to manage users and organizations. #7196
• Added tooltips to explain the task actions "Reset" and "Reset and Cancel". #7201
• Thumbnail improvements: Thumbnails now use intensity configuration, thumbnails can now be created for float datasets, and they are cached across webknossos restarts. #7190

Changed

• Redesigned the info tab in the right-hand sidebar to be fit the new branding and design language. #7110
• The proofreading tool is always visible now (even when disabled). #7174
• Optimized processing of parallel requests (new thread pool configuration, asynchronous FossilDB client), improving performance and reducing idle waiting. #7139
• Renamed "open" tasks to "pending" and slightly redesigned the available task assignment view for clarity. #7187
• Being the uploader of a dataset no longer grants edit permissions on that dataset. #7200
• Enabled the "Shift + middle-click" shortcut to load agglomerate skeletons for all tools, not just the Skeleton tool. #7212

Fixed

• Fixed rare rendering bug at viewport edge for anisotropic datasets. #7163
• Fixed the dataset search which was broken when only the root folder existed. #7177
• Correctly use configured fill-value for missing chunks of remote datasets hosted on gcs or s3. #7198
• Correctly use configured fill-value for missing chunks of local non-wkw datasets. #7216
• Adapted the proofreading docs to reflect the current state of the proofreading tool. #7212
• Fixed a bug when adding remote datasets while not having write-access to the root folder. #7221

Removed

• Removed the "Globalize Floodfill" feature that could extend partial floodfills across an entire dataset. Please use the fill tool multiple times instead or make use of the proofreading tool when correcting large structures. #7173

23.07.0

• Docker Image scalableminds/webknossos:23.07.0 🐳
  Run it via export DOCKER_TAG=="23.07.0" && ./start-docker.sh.
• Changelog
• Commits

Highlights

• Added new shortcuts for fast tool switching. Look at the updated Keyboard Shortcuts documentation to see the new shortcuts. #7112
• Creating bounding boxes can now be done by dragging the left mouse button (when the bounding box tool is selected). To move around in the dataset while this tool is active, keep ALT pressed. #7118

Added

• Subfolders of the currently active folder are now also rendered in the dataset table in the dashboard. #6996
• Added ability to view zarr v3 datasets. #7079
• Added an index structure for volume annotation segments, in preparation for per-segment statistics. #7063
• Instead of showing all possible action items next to each other, there is now an overflow menu for layer actions. #7123

Changed

• Agglomerate skeletons can only be modified if the proofreading tool is active so they stay in sync with the underlying segmentation and agglomerate graph. Agglomerate skeletons cannot be modified using any other means. They are marked in the skeleton list using the clipboard icon of the proofreading tool. When exporting skeletons in the NML format, trees ("things") now have a type property which is either "DEFAULT" or "AGGLOMERATE". #7086
• The cache for remote dataset array contents can now have a configured size in bytes. New config option datastore.cache.imageArrayChunks.maxSizeBytes. Default is 2 GB, consider increasing for production. #7067
• Optimized processing of parallel requests for remote datasets, improving performance and reducing idle waiting. #7137

Fixed

• Fixed a bug where some volume annotations could not be downloaded. #7115
• Fixed reading of some remote datasets where invalid data would follow valid gzip data, causing the decompression to fail. #7119
• Fixed problems which could arise when annotating volume data at negative positions (which is not supported and is properly ignored now). #7124
• Fixed some requests failing for streaming remote data via HTTP, which was observed when streaming data via Zarr from another WEBKNOSSOS instance. #7125
• Fixed that the brush preview was inaccurate in some scenarios. #7129
• Fixed order of decompression on neuroglancer precomputed datasets, which caused some segmentation layers to not load correctly. #7135

Removed

• Support for webknososs-connect data store servers has been removed. Use the "Add Remote Dataset" functionality instead. #7031

23.06.0

• Docker Image scalableminds/webknossos:23.06.0 🐳
  Run it via export DOCKER_TAG=="23.06.0" && ./start-docker.sh.
• Changelog
• Commits

Highlights

• Added a machine-learning based quick select mode. Activate it via the "AI" button in the toolbar after selecting the quick-select tool. #7051
• Added segment groups so that segments can be organized in a hierarchy (similar to skeletons). #6966
• Added a new "cover" blend mode which renders the visible layers on top of each other. The new blend mode can be selected in the Data Rendering settings in the settings tab of the left side bar. #6936

Added

• In addition to drag and drop, the selected tree(s) in the Skeleton tab can also be moved into another group by right-clicking the target group and selecting "Move selected tree(s) here". #7005
• Added support for remote datasets encoded with brotli. #7041
• Teams can be edited more straight-forwardly in a popup in the team edit page. #7043
• Added support to download layers of a dataset as (OME) TIFF files in the download modal when viewing a dataset. #7068
• Annotations with Editable Mappings (a.k.a Supervoxel Proofreading) can now be merged. #7026
• The file size and inodes of artifacts are now aggregated and shown in the Voxelytics workflow list. #7071
• It is possible to disable the automatic loading of meshes during proofreading. ##7076
• When viewing a public dataset by another organization, the organization is shown next to the dataset list, and when viewing the dataset or an annotation. #7087

Changed

• Loading of precomputed meshes got significantly faster (especially when using a mesh file for an oversegmentation with an applied agglomerate mapping). #7001
• Improved speed of proofreading by only reloading affected areas after a split or merge. #7050
• The minimum length of layer names in datasets was set from 3 to 1, enabling single-character names for layers. #7064
• All dataset managers are now allowed to see all voxelytics workflow reports created in their organization. Previously, only admins could see all workflow reports, with other users seeing only their own. #7080
• Improved performance for large meshes, especially when loaded from a precomputed oversegmentation mesh file. #7077
• Slight increased the spacing and width of some VX reports elements. #7094

Fixed

• Fixed that changing a segment color could lead to a crash. #7000
• The fill_value property of zarr dataset is now used when it is not a number. #7017
• Fixed a bug that made downloads of public annotations fail occasionally. #7025
• Fixed layouting of used storage space on the organization page. #7034
• Fixed a bug where updating skeleton annotation tree group visibility would break the annotation. #7037
• Fixed importing Neuroglancer Precomputed datasets that have a voxel offset in their header. #7019, #7062
• Fixed reading Neuroglancer Precomputed datasets with non-integer resolutions. #7041
• Fixed a bug where invalid email addresses were not readable in dark mode on the login/signup pages. #7052
• Fixed a bug where users could sometimes not access their own time tracking information. #7055
• Fixed a bug in the wallTime calculation of the Voxelytics reports. #7059
• Fixed a bug where thumbnails and raw data requests with non-bucket-aligned positions would show data at slightly wrong positions. #7058
• Avoid crashes when exporting big STL files. #7074
• Fixed rare rendering bug for datasets with multiple layers and differing magnifications. #7066
• Fixed a bug where duplicating annotations with Editable Mappings could lead to a server-side endless loop. #7026
• Fixed the datasource-properties.json route for zarr-streaminge export of datasets that are not wkw/zarr. #7065
• Fixed an issue where you could no longer invite users to your organization even though you had space left. #7078
• Fixed displayed units of used storage in the organization's overview page. #7057
• Fixed a rendering bug that could occur when a dataset layer has missing mags (e.g., the first mag is 8-8-8). #7082
• Fixed a bug where some volume annotations could not be duplicated or used as tasks. #7085
• Fixed a superfluous rectangular geometry rendered at 0,0,0. #7088

23.05.2

• Docker Image scalableminds/webknossos:23.05.2 🐳
  Run it via export DOCKER_TAG=="23.05.2" && ./start-docker.sh.
• Changelog
• Commits

Fixed

• Fixed a bug where users could sometimes not access their own time tracking information. #7055

23.05.1

• Docker Image scalableminds/webknossos:23.05.1 🐳
  Run it via export DOCKER_TAG=="23.05.1" && ./start-docker.sh.
• Changelog
• Commits

Fixed

• Fixed rendering issues on some affected systems that led to "black holes". #7018
• Added a workaround for a WebGL crash which could appear when a dataset contained many segmentation layers. #6995

23.05.0

• Docker Image scalableminds/webknossos:23.05.0 🐳
  Run it via export DOCKER_TAG=="23.05.0" && ./start-docker.sh.
• Changelog
• Commits

Highlights

• Segments can now be removed from the segment list via the context menu. #6944
• Added support for viewing neuroglancer precomputed segmentations using "compressed segmentation" compression. #6947

Added

• WEBKNOSSOS screenshots now include a logo in the lower left corner. Users with a paid license can disable this feature in the viewport options in the settings tab on the left side of the screen. #6910
• Added support for datasets with mixed magnifications (e.g., one layer contains mag 2-2-2 and another contains 2-2-1). #6943
• Added rendering precomputed meshes with level of detail depending on the zoom of the 3D viewport. This feature only works with version 3 mesh files. #6909
• Editing the meta data of segments (e.g., the name) is now undoable. #6944
• Added more icons and small redesigns for various pages in line with the new branding. #6938
• Added more graphics and branding to job notification emails. #6994
• Added action button in Team Admin page that links to the User Admin page to edit team members there. #6958

Changed

• Moved the view mode selection in the toolbar next to the position field. #6949
• Redesigned welcome toast for new, annonymous users with new branding. #6961
• When saving annotations, the URL of the webknossos instance is stored in the resulting NML file. #6964

Fixed

• Fixed unintended dependencies between segments of different volume layers which used the same segment id. Now, using the same segment id for segments in different volume layers should work without any problems. #6960
• Fixed incorrect initial tab when clicking "Show Annotations" for a user in the user list. Also, the datasets tab was removed from that page as it was the same as the datasets table from the main dashboard. #6957
• Fixed that unsaved changes were shown when opening an annotation, although there weren't any. #6972
• Fixed misleading email about successful dataset upload, which was in some cases sent even for unusable datasets. #6977
• Fixed upload of skeleton annotations with no trees, only bounding boxes, being incorrectly rejected. #6985
• Fixed that Google Cloud Storage URLs with bucket names containing underscores could not be parsed. #6998
• Fixed regression that caused public datasets to crash when not being logged in. #7010