We use probabilistic algortihms to segment 3D microscopy images, which makes it possible to automatically process lower quality mammalian tissue and organoid samples, than required for alternative algorithms. Software also allows to manually define regions in space, which enable investigating geometric protein distribution within tissue and inter-protein relationships. Software is free to use and download after signing in.
In vitro production of organ mimicking 3D tissues holds a promise for efficient drug screening strategies. Currently analysis is limited to brighfield microscopy. Here we explore how to automatically analize stem cell spheroids.
Even though the field of mouse pre-implantation biology is more than a century old, these developing tissues still reveal surprising details, in addition being a perfect playground for new image analysis algorithms.
Post-implantation embryonic stages involve some of the most dramatic changes in tissue shape and biochemical composition. 3D analysis is crucial to understand how growing tissues self organise and generate complexity.