scalable minds GmbH

scalable minds GmbH is a German software company based in Potsdam that develops tools and services for working with very large biomedical image datasets. Its best-known product is WEBKNOSSOS, an open-source web platform for viewing, annotating and analyzing large-scale image data. According to the company's own description, WEBKNOSSOS lets users visualize gigabyte- to petabyte-sized 2D and 3D datasets online, annotate them collaboratively (skeletons and segmentation), securely share datasets with collaborators, and work with data optimized for 3D microscopy and MRI/CT scans. The platform is offered with a free entry point ("Get started for free") alongside commercial services. Beyond the WEBKNOSSOS software, scalable minds positions itself as a service provider for image analysis and reconstruction projects. Its service portfolio includes neuron segmentation and connectome reconstruction, volume electron microscopy alignment and stitching, normalization and gradient correction, Zarr consulting, and custom AI services. The company states that its segmentation and reconstruction services are based on Voxelytics technology, and that it has implemented full Zarr support in both WEBKNOSSOS and Voxelytics. Its stated mission is to connect domain experts with the latest machine learning expertise, and it emphasizes that its technology stack scales from gigabyte-sized to petabyte-sized datasets. The company's customer base is scientific. Testimonials on its website come from researchers at institutions such as the Max Planck Institute for Brain Research and the Francis Crick Institute, and its services are aimed at domains including bioimaging (with OME-Zarr), neuroscience, connectomics, and other fields that deal with large n-dimensional data. Typical applications mentioned include segmentation of biological features such as neurons, cells and membranes, identification of cell organelles, detection of damaged tissue and lesions, and automatic counting and measurement of identified structures. Supported imaging modalities include 2D and 3D electron microscopy, MRI and CT, synchrotron X-ray and micro-CT, confocal fluorescence microscopy and light microscopy. scalable minds is a private company. Wikidata describes it simply as a company in Potsdam, Germany. It is active in the open-source and open-standards communities around scientific data, notably the Zarr community, where it says it helps develop the specification and library implementations. The company also recruits publicly, advertising open positions on its website.

scalable minds GmbH is a company based in Potsdam, Germany, as recorded in Wikidata. Public evidence available here does not specify its founding date or founders, but the company presents itself as having "years of experience in image analysis and reconstruction projects" and as a developer of scientific software used by major research institutions. The company's central product, WEBKNOSSOS, is an open-source web platform for viewing, annotating and analyzing large-scale image datasets. It supports visualization of gigabyte- to petabyte-sized 2D and 3D datasets online, collaborative annotation via skeletons and segmentation, secure dataset sharing, and is optimized for 3D microscopy and MRI/CT scans. WEBKNOSSOS is offered with a free entry point and is used by researchers; testimonials on the company's website come from the Max Planck Institute for Brain Research and the Francis Crick Institute, among others. Alongside WEBKNOSSOS, scalable minds developed Voxelytics technology, which underpins its neuron segmentation and connectome reconstruction service. The company describes this service as automatically reconstructing biological features from 2D or 3D image datasets, covering tasks such as segmenting, measuring, locating and counting, connectome reconstruction, and analysis of neurons, cell organelles, synapses, lesions and tissue. Over time the company expanded into a broader service business. Its portfolio includes a volume electron microscopy alignment service (3D alignment and registration, 2D in-plane stitching and montages, normalization and gradient correction), Zarr consulting, and custom AI services. The alignment service is offered as a full service requiring no coding: customers upload a dataset and receive results, with features such as dynamic mesh transformations, masking for arbitrary shapes, RANSAC-based global alignment, and robust outlier detection. In the area of data formats, scalable minds has become active in the Zarr community. It states that it helps develop the Zarr specification and library implementations, and that it has implemented full Zarr support in WEBKNOSSOS and Voxelytics. Its Zarr consulting offering covers integrating Zarr support into customer software, optimizing Zarr data for specific use cases, distributed computing in the cloud or on HPC, best-practice consulting, collaboration on specifications and community work, and workshops. The company's custom AI services extend its standardized preprocessing, alignment, segmentation and reconstruction offerings. It describes a mission to connect domain experts with the latest machine learning expertise, and says it can deliver a full service including training data generation, model development and proof-reading, with a technology stack scaling from gigabyte- to petabyte-sized datasets. Supported imaging modalities span 2D and 3D electron microscopy, MRI and CT, synchrotron X-ray and micro-CT, confocal fluorescence microscopy and light microscopy. The company continues to operate and recruit, advertising job openings on its website.

Scientific software and services provider for large-scale biomedical image analysis, combining an open-source platform (WEBKNOSSOS) with expert consulting and AI-driven reconstruction services.

• WEBKNOSSOS

  Open-source web platform for viewing, annotating and analyzing large-scale image datasets; supports gigabyte- to petabyte-sized 2D and 3D datasets, collaborative skeleton and segmentation annotation, secure sharing, and is optimized for 3D microscopy and MRI/CT scans.

• Voxelytics

  Technology underlying scalable minds' neuron segmentation and connectome reconstruction service; full Zarr support has been implemented in it.

• Neuron Segmentation & Connectome Reconstruction Service

  Service that automatically reconstructs biological features from 2D or 3D image datasets, based on Voxelytics technology; covers segmenting, measuring, locating and counting, connectome reconstruction, and analysis of neurons, cell organelles, synapses, lesions and tissue.

• Volume EM Alignment Service

  Full service for alignment of 3D electron microscopy datasets and 2D in-plane stitching and montages, with dynamic mesh transformations, masking, RANSAC-based global alignment, robust outlier detection, and normalization and gradient correction; no coding required.

• Zarr Consulting

  Consulting on the Zarr chunked, cloud-native storage format, including integrating Zarr support into customer software, optimizing Zarr data, distributed computing in the cloud or on HPC, best-practice consulting, specification and community collaboration, and workshops.

• Custom AI Services

  Flexible AI solutions matching customer data and image analysis needs, including training data generation, model development and proof-reading; examples include segmentation of biological features, cell organelle identification, detection of damaged tissue and lesions, and automatic counting and measurement.

1. 1scalable mindsscalableminds.com
2. 2scalable minds | Zarr Consultingscalableminds.com
3. 3scalable minds | Volume EM Alignment Servicescalableminds.com
4. 4scalable minds | Custom AI Servicesscalableminds.com
5. 5scalable minds GmbH (Germany) - Wikidatawikidata.org