Pioneering Accessibility in Retinal Connectomics

INTERVIEW - May 2024

In this interview with Prof. David Berson from Brown University, you will learn about his pioneering research on the retina, how EM-based connectomics has influenced his work, and get insights into his latest project. Read more.

A story about collaboration, continents, and the struggles of big data

VIDEO - April 2024

Embark on a journey with two scientists in London as they navigate the challenges of managing large datasets from a serial electron microscope. Read more.

Behind the scenes of WEBKNOSSOS

INTERVIEW - February 2024

Philipp Otto has been one of the principal developers of WEBKNOSSOS for a decade. In this interview, he will share his story and insights from behind the scenes of developing such a product, including the challenges and the enjoyment it brings. Read more.

Feature highlights of WEBKNOSSOS from 2023

FEATURE - January 2024

2023 was a year full of new features for WEBKNOSSOS, with exciting additions: from AI-powered quick-select tools to improved touch device support, here are the standout features we want to make sure you haven’t missed! Read more.

Creating animations with WEBKNOSSOS

FEATURE - December 2023

We are excited to introduce a new feature in WEBKNOSSOS for creating professional-looking animations of your data. Read more.

Segment Statistics in WEBKNOSSOS

FEATURE - October 2023

You can now access segment statistics in WEBKNOSSOS! The segments statistics include essential information like cell count, the volume of the segments, their positions, as well as their bounding boxes. Read more.

Introducing 4D datasets for time series in WEBKNOSSOS

FEATURE - September 2023

WEBKNOSSOS added support for time series datasets, opening up a new dimension in your data exploration. Now, you can not only view your data in 3D but also in 4D, adding the element of time. Read more.

Showing and annotating data with an iPad

TUTORIAL - August 2023

Using WEBKNOSSOS on an iPad offers two key advantages: seamless data visualization on the go and intuitive annotation with the Apple Pencil. Discover in this tutorial how to show and annotate your data with an iPad. Read more.

Pen Tablets and WEBKNOSSOS

TUTORIAL - July 2023

In this tutorial, we share helpful tips on using pen tablets for efficient data annotation with WEBKNOSSOS. You will learn to program your tablet and pen buttons to match the WEBKNOSSOS shortcuts and we will show you a complete annotation workflow. Read more.

Comparative Connectomic Studies among Species

INTERVIEW - July 2023

Sahil Loomba is a post-doctoral research scientist at the Max Planck Institute for Brain Research. In this interview, he will discuss the research’s origins, the encountered challenges, the tools and techniques employed, and his perspective on the future development of comparative connectomics across not only species, but also ages and disease models. Read more.

New AI-based quick segment tool in WEBKNOSSOS

FEATURE - June 2023

We are excited to announce the integration of Meta’s new AI model, SAM: Segment Anything, into WEBKNOSSOS! Learn how to make the best out of the AI option in WEBKNOSSOS. Read more.

Automation and interoperability

TUTORIAL - June 2023

In this tutorial, we will learn how to download data as a Tiff stack with the WEBKNOSSOS UI, how to automate this process, and how to incorporate an N5 remote dataset into WEBKNOSSOS. Read more.

Volume annotations with WEBKNOSSOS

TUTORIAL - May 2023

In this tutorial, we will explore the annotation features of WEBKNOSSOS. We will cover everything from opening and annotating a published dataset to utilizing both basic and advanced annotation tools. Read more.

Data sharing with WEBKNOSSOS

TUTORIAL - April 2023

In this tutorial, you will discover how to efficiently manage and share your data. Read more.

Self-hosted data for WEBKNOSSOS

TUTORIAL - February 2023

This tutorial explains how to store data externally by converting data into OME-Zarr and setting up a static file server for use with WEBKNOSSOS. Read more.

Organize your data in folders

FEATURE - February 2023

The folder structure in WEBKNOSSOS allows you to have your datasets structured, organized, and easily accessible. Read more.

Rebranding WEBKNOSSOS

STORY - February 2023

Follow our journey of redesigning the branding of WEBKNOSSOS to align it more closely with our identity and values. Read more.

Feature highlights of WEBKNOSSOS from 2022

FEATURE - February 2023

Read all about the top features of 2022: quick-select, interpolation tool, collaborative annotations, and more. Read more.

Comparing Array Tomography with Serial Block-face Electron Microscopy

EXPERIMENT - January 2023

Array tomography and Serial Block-face Electron Microscopy are two microscopy techniques that work in a similar way and are hard to understand. We playfully explained and compared these techniques using a fig (AT) and a tomato (SBEM). Read more.

Reconstructing a kiwi fruit… with SBEM (sort of)

EXPERIMENT - January 2023

How would you explain SBEM/volume EM and 3D reconstruction to your grandparents? With a camera, a knife, and a kiwi fruit. Read more.

Data Streaming with WEBKNOSSOS Libs

TUTORIAL - November 2022

Today, we would like to highlight some features and quality of life improvements WEBKNOSSOS acquired over the summer. They will accelerate your workflows and make the annotating of EM data easier. Read more.

Using Zarr Datasets with WEBKNOSSOS

TUTORIAL - October 2022

This tutorial explains how to load any Zarr-format-based datasets into WEBKNOSSOS. We support reading Zarr dataset from the local file system, cloud providers such as S3 and Google Cloud, as well as through any web server over HTTP. Read more.

Zarr Streaming from WEBKNOSSOS

TUTORIAL - September 2022

In this blog post, we will share some progress on streaming any dataset from WEBKNOSSOS to compatible third-party programs through the Zarr interface. Read more.

Summer update: annotate faster than ever with these new features

FEATURE - August 2022

Today, we would like to highlight some features and quality of life improvements WEBKNOSSOS acquired over the summer. They will accelerate your workflows and make the annotating of EM data easier. Read more.

Interview with Carles Bosch on Correlative Multimodal Imaging

INTERVIEW - July 2022

Carles Bosch, principal laboratory research scientist at the Sensory Circuits and Neurotechnology Laboratory of the Francis Crick Institute, explains his research on glomerular column circuits in the mouse olfactory bulb. Read more.

Reconstructing connectomes from human, macaque, and mouse cortex with Voxelytics

INTERVIEW - July 2022

Daniel Werner, data scientist at scalable minds, tells us about the analysis and reconstruction of 9 vEM datasets he contributed to for a comparative connectomic study among species, by the Max Planck Institute for Brain Research. Read more.

How to speed up your annotations using the volume interpolation tool in WEBKNOSSOS

FEATURE - June 2022

In this tutorial, we will tell you about the interpolation feature. Draw on one slice, move forward by a few slices, draw again… and WEBKNOSSOS will interpolate the segments between the two annotated slices. Read more.

How to debug a synapse classifier with WEBKNOSSOS

INTERVIEW - October 2021

Today, we will have a chat with one of our colleagues: Valentin Pinkau. As an experienced data scientist specializing in connectomics, he has some interesting insights to share. Read more

Automated Neuron Reconstruction

CASE STUDY - August 2021

With the recent publication of the “Dense connectomic reconstruction in layer 4 of the somatosensory cortex“ paper by the Max-Planck-Institute for Brain Research, we showcase WEBKNOSSOS and the ML reconstruction pipeline Voxelytics. Read more

Machine learning workflows for large-scale reconstruction projects

TUTORIAL - July 2021

Here, we share some tips on how to reconstruct biological objects (e.g. neurons) from tera- or peta-scale image datasets. Read more.