Scientific Computing's bioimage analysis projects at the John Innes Centre
jicbioimage: a tool for automated and reproducible bioimage analysis
Python tool that allows users to quickly view and explore microscopy data; generate reproducible analyses, encoding a complete history of image transformations from raw data to final result; and scale up analyses from initial exploration to high throughput processing pipelines, with a minimal amount of extra effort.
RNA FISH probe counting
Software to assist with the enumeration of single molecule RNA probes. It operates on microscope data files, eventually outputting an annotated image showing a projection of the data with suggested cell boundaries and probe counts and areas (in pixels) for those cells.
Root reconstruction and nuclear intensity analysis
This code implements a quantitative image analysis pipeline for the reconstruction of root cell volumes from confocal microscopy data. These reconstructed cell volumes can be used to measure fluorescence intensity in other channels in the confocal images.