Image visualisation

The BigDataViewer is a re-slicing browser for terabyte-sized multi-view image sequences. BigDataViewer was developed with multi-view light-sheet microscopy data in mind and integrates well with Fiji's SPIMage processing pipeline.

BioImageXD is a free open source software package for analyzing, processing and visualizing multi-dimensional microscopy images. It's a collaborative project, designed and developed by microscopists, cell biologists and software engineers from the Universities of Jyväskylä and Turku in Finland, Max Planck Institute CBG in Dresden, Germany and collaborators worldwide. BioImageXD was published in the July 2012 issue of Nature Methods.

Advanced Cell Classifier is a data analyzer program to evaluate cell-based high-content screens and tissue section images developed at the Biological Research Centre, Szeged and FIMM, Helsinki (formerly at ETH Zurich). The basic aim is to provide a very accurate analysis with minimal user interaction using advanced machine learning methods.

ASAP is an open source platform for visualizing, annotating and automatically analyzing whole-slide histopathology images. It consists of several key-components (slide input/output, image processing, viewer) which can be used seperately. It is built on top of several well-developed open source packages like OpenSlide, Qt and OpenCV but also tries to extend them in several meaningful ways.

arivis Vision4D is a modular software for working with multi-channel 2D, 3D and 4D images of almost unlimited size independent of available RAM. Many imaging systems, such as high speed confocal, Light Sheet/ SPIM and 2 Photon systems, can produce a huge amount of multi-channel data, which arivis Vision4D handles without constraints. Terabyte ready arivis Vision4D main functionality: Easy import of most image formats from microsopes as well as biological formats High performance interactive 3D / 4D rendering on standard PCs and laptops with 3D Graphics Support Intuitive tools for stitching and alignment to create large multi-dimensional image stacks Immediate 2D, 3D and 4D visualization, annotation and analysis regardless of image size Creation, import, and export of 4D Iso-surfaces Powerful Analysis Pipeline for 3D /4D image analysis (cell segmentation, tracking, annotation, quantitative measurement and statistics, etc) Semi-automatic/manual segmentation and tracking with interactive Track Editor Easy design and export of 3D / 4D High Resolution Movies Seamless integration of custom workflows via Matlab API and Python scripting Data sharing for collaboration A user friendly software, easy to learn and use for any life scientist