FEATURE

Summer update: annotate faster than ever with these new features

Albane le Tournoulx de la Villegeorges

Aug 2022

Today, we would like to highlight some awesome features and quality of life improvements webKnossos acquired over the summer. They will accelerate your workflows and make the annotating of EM data easier… so make sure you did not miss any of them! Here is a small overview we prepared to keep you in the loop.

HIGHLIGHTS

Shared annotation feature

With the new team sharing feature of webKnossos, you can invite team members to edit your annotation. You will be working on a single annotation together, without having to send around versions. Working collaboratively on one dataset has never been this easy!

Inviting and sharing an annotation with other team members for collaborative editing.

For more clarity, we decided to replace the tab “my annotations” with “shared annotations”. Each member of your team will automatically have access to all shared annotations from their dashboard so that you will not need to send links around anymore.

New annotation tab containing both your private and team-shared annotations in webKnossos.

Volume interpolation and extrusion

The newly released volume interpolation tool is one of the most time-saving features for annotating EM data. Segmenting cells on each slice of data is incredibly time-consuming. The interpolation tool allows you to skip some of them.

All you have to do is to draw on one slice, move forward by a few slices, draw again… and the in-between slices will be annotated automatically through interpolation.

Interpolating a segment between slices.

Alternatively, you can extrude (copy) a single segment to one or more slices without any interpolation between the starting and ending slices. This is great for straight tube-like features.

Extruding a single segment for a few slices.

Zarr streaming

We have recently expanded webKnossos such that any dataset and annotation in webKnossos can be shared, accessed, and streamed to other third-party programs and libraries that understand the Zarr interface (e.g. Neuroglancer, Fiji, Napari).

Opening the same dataset in webKnossos and then in Neuroglancer streamed from webKnossos.

IMPROVEMENTS TO MAKE ANNOTATING EASIER

Context-sensitive mouse pointer

The mouse cursor now changes appearance: brush, eraser, lasso, flood fill… This is of great help to never forget which annotation tool you have selected.

Active tool indicated by the mouse cursor.

Re-enabling tool

webKnossos will from now on remember which annotation tool was last used. Let’s say, for example, that you are segmenting cells with the brush tool and you quickly want to have a look at the raw data. You toggle the visibility of the layer with the keyboard shortcut “3”. As you turn the segmentation layer on, webKnossos will remember the active tool — in the example below the brush tool — and you can directly continue to annotate.

Brushing and toggling the layer’s visibility: brush tool stays active after toggling.

Download speed indicator

You can now view the download speed of the image data when navigating through your datasets in webKnossos. In the status bar, you will find a download speed indicator and when hovering, the total amount of downloaded data.

Looking at the download speed indicator and the total amount of downloaded data.

FOR PRO-USERS

Ad hoc meshing

Remember when you edited a segmentation layer and could not compute the meshes of your new segments? Well, that’s over now! The ad hoc meshing for volume annotation works with edited as well as existing segmentation layers. Simply right-click on the new mesh and choose “compute mesh”.

Editing an existing segmentation layer, computing the new segment, and loading the mesh of an existing one.

UI to download/export a dataset in view-mode

You can now download whole datasets in webKnossos using the Python library. Just follow the steps indicated in the UI and integrate them in your own scripts.

Opening the Python Client modal to download datasets.

Extended features for Connectomics

Have you heard of Voxelytics yet, our AI system for neuron reconstruction? Our customers and partners using Voxelytics have access to additional features in webKnossos to accelerate their work. Here are some of them:

Proof-reading mode

With the new proof-reading mode, you can split or merge agglomerate skeletons and follow the changes in real-time: they will be visible in the mesh and segmentation.

Fixing a merge error with the proof-reading mode in webKnossos.

Fixing a split error with the proof-reading mode in webKnossos.

Connectome explorer

With the interactive connectome explorer, you can explore a neuron’s synaptic connections, inspect all its individual, outgoing synapses with their types indicated, jump to their location, and load the synaptic partners of the initial segment. This is an incredibly powerful analysis tool for research in connectomics.