Resource Library

Successor of SR-Tesseler and Coloc-Tesseler, Point Cloud Analyst is an interactive software platform that allows the quantification of multi-dimensional and multi-colour point clouds data, with a focus on single-molecule localisation microscopy data.

Coloc-Tesseler is an interactive software platform that allows co-localisation analysis of 2D and 3D localisation microscopy data.

ParticleSpy is a Python package that eases segmentation and analysis of nanoparticles from electron microscopy data. It is built on the HyperSpy package and can be used with any data loaded via HyperSpy.

PyTorch-3dunet is an easy-to-use package for training neural networks to solve 2D and 3D segmentation problems

riCOM provides real-time image reconstruction methods for scanning transmission electron microscopy (STEM).

NanoJ is an open-source toolbox for super-resolution microscopy data analysis. It encompasses several essential processing steps; spatiotemporal alignment of raw data (NanoJ-Core), super-resolution image reconstruction (NanoJ-SRRF), image quality assessment (NanoJ-SQUIRREL), structural modelling (NanoJ-VirusMapper) and control of the sample environment (NanoJ-Fluidics).

Superresolution Microscopy Analysis Platform (SMAP) is a freely available all-in-one analysis package for single molecule localisation microscopy data.

This is an open-source suite to mathematically model turnover rates in an intervention-free manner given the ability to quantify mRNA and protein expression from initiation to homeostasis.

ZeroCostDL4Mic is an open-source toolbox of deep learning-based tools for microscopy image processing and analysis.

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.

pyxem is an open-source Python library for multi-dimensional diffraction microscopy. It has been primarily developed as a platform for hybrid diffraction-microscopy based on 4D scanning diffraction microscopy data in which a 2D diffraction pattern is recorded at every position in a 2D scan of a specimen.

Analysis code for AFM raw data post-processing and Hertz model calculation to obtain Young's modulus for increasing indentation depths.

TrackPy is a Python package for particle tracking in 2D, 3D and higher dimensions. It can be used at a range of length scales and applied to image stacks recorded using both light microscopy and electron microscopy.

abTEM is a pure Python code for running simulations of (scanning) transmission electron microscopy images using the multi -slice or PRISM algorithms. It is open-source, blazing fast, and extremely versatile and easy to extend.

IPyvolume is a Python library to visualise 3D volumes and glyphs (e.g., 3D scatter plots), in Jupyter notebooks with minimal configuration and effort.

DECODE is a Python and Pytorch based deep learning tool for high density 3D single molecule localisation microscopy (SMLM) analysis.

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.