FEATURE

Feature highlights of WEBKNOSSOS from 2022

Albane le Tournoulx de la Villegeorges

Feb 2023

The visualization, sharing and annotation capabilities of WEBKNOSSOS have grown a lot over the last year. In this article, we will be revisiting some of our favorite features. Have look and make sure you have not missed anything!

The interpolation feature

Annotate a cell, skip a few slices and annotate it again. Use the interpolation tool to have WEBKNOSSOS segment it in 3D!

Using the interpolation tool for a cell annotated on two separate slices.

The quick-select tool

Simply draw a rectangle around a cell and voila! It’s annotated. Try it out in combination with the interpolation tool for even more efficient results.

Segmenting a kiwi fruit with the quick-select feature.

Custom color segments

Change the colors of segments in WEBKNOSSOS. Make cells blue, pink, even black or white! This is great for differentiating cells in your segmentation.

Changing the colors of segments.

Proof-reading tool

Simply click on a location in your annotation and right-click on another one to merge or split segments.

Splitting a segment with the proof-reading tool based on an over-segmentation. Read more on how to use the proof-reading tool here.

Team sharing

You can allow members of your team to edit your annotation and work on a single annotation together, without having to send around versions.

Allow collaborator to edit the annotation.

Dataset tags

Filter your datasets with tags depending on their attributes or specifications using the dataset tags.

Example of dataset tags.

Folder structure for datasets

Organize your datasets in different folders and attach user permissions to each folder. This will help you manage your data, even when your organization is handling hundreds of datasets!

Organizing datasets in folders in WEBKNOSSOS.

Mesh and layout in sharing link

The currently visible meshes and the layer configuration are part of the sharing link — the recipient will see the exact same thing as you!

Computing meshes, sharing the annotation and open it.

Short links

The sharing links of WEBKNOSSOS became shortened by default. So much data in just a few characters!

Sharing an annotation: the sharing link is shortened.

Datasets exposed as Zarr arrays

Any dataset and annotation in WEBKNOSSOS can be streamed to other third-party programs that understand the Zarr interface (e.g. Neuroglancer, Fiji and Napari). Additionally, you can also load any Zarr-format-based datasets into WEBKNOSSOS.

Viewing a dataset in WEBKNOSSOS and opening it in Neuroglancer.

Connectome viewer

Select a segment, and a list of its synaptic connections and partners will appear. Click on a synapse, and the viewports will jump to its location. The easiest way to explore a connectome!