Teaching Data Science, Biostats and Bioinformatics

AFT is an open-source workflow to quantify alignment of fibrillar features in bioimages. It allows for evaluation of alignment lengthscale and works with a number of different imaging modalities.

py4DSTEM is a Python toolkit for analysis and visualisation of 4D-STEM data.

TomoPy is an open-source Python package for tomographic data processing and image reconstruction.

SR-Tesseler is an open-source interactive single molecule localisation microscopy clustering tool based on Voronoï tesselation, that allows for segmentation and quantification of localisation-based super-resolution microscopy data.

PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline is tuned for images acquired with confocal and light sheet microscopy and can be used to segment both plant and animal tissues.

StatSTEM provides a user-friendly way of quantifying atomic-resolution scanning transmission electron microscopy (STEM) images by using parametric model-based fitting. In this manner, accurate and precise quantitative information can be extracted about the material under investigation.