The webKnossos team builds collaborative image analysis tools for life sciences

webKnossos is the result of a collaboration between neuroscientists at the Max Planck Institute for Brain Research and engineers at scalable minds

The scientists from the Helmstaedter lab at the Max Planck Institute for Brain Research are working on Connectomics projects to gain insights from the neural wiring of the mammalian brain. For that, they acquire multi-terabyte 3D electron microscopy image datasets. To extract insights from the data, a collaboration of many annotators is required. Since there were no online tools available, the team was sending out hard drives to their annotators in order to distribute the work.To facilitate and scale annotation efforts, the group collaborated with scalable minds and initiated the development of webKnossos. In this collaboration, the scientists shaped the core features including the annotation tools and the task management system. Today, webKnossos is their workhorse tool for scientific discoveries in large image datasets. Check out recent publications in our publication gallery.


scalable minds is a team of professional software and data engineers based in Potsdam, Germany. The team brought their technical expertise to the project. They architected the data streaming infrastructure, which enables fast data browsing in even the largest image datasets. With the addition of the high-performance GPU-based rendering, the unique flight mode for fast neurite annotation was made possible. In collaboration with the team at the Max Planck Institute for Brain Research, they developed webKnossos and contributed to the publication in Nature Methods.scalable minds actively develops webKnossos and adds new features every month. In addition to the development of webKnossos, the company provides services for hosting, manual annotations, image stack alignment, and automated segmentation to the scientific community and industry.


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