Online Microscopy Resources

Prismatic is a CUDA/C++/Python GPU+CPU software package for fast image simulation in high resolution and scanning transmission electron microscopy (HRTEM & STEM) that includes a graphic user interface.

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.

OpenPNM is an open-source pore network modelling package providing for a wide variety of pore-scale simulation tasks. It is designed to be fully agnostic to the topology and dimensionality of network by using graph theory representations to describe the architecture.

MorphoLibJ is a collection of mathematical morphology methods and plugins for ImageJ (morphological filtering/reconstruction, watershed segmentation, 2D/3D measurements, binary/label images utilities).

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.

PoreSpy is a collection of image analysis tools used to extract information from 3D images of porous materials.

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.

Atomap is a Python library for analysing atomic resolution scanning transmission electron microscopy images. It relies on fitting 2D Gaussian functions to every atomic column in an image, and automatically finds all major symmetry axes.

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.

TRABI (temporal, radial-aperture-based intensity estimation) is a free ImageJ macro used for 3D processing of 2D single molecule microscopy data. Through intensity estimation in different regions of the emission pattern of single fluorophores, a relative 3D position can be determined from 2D data with no adaptation to the microscope.