Resource Library

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

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.

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.

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.

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

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.

Microscopy Image Browser (MIB) is a package for image processing, segmentation, and visualisation of multi-dimensional (2D-4D) microscopy datasets.

StarDist is an AI-based tool for object detection with star-convex shapes in 2D and 3D. Intended for cell nuclei detection/segmentation in microscopy images, it can be used via the stand-alone Python software package, or with the provided plugins for other common image analysis software suites (e.g., Fiji, napari, QuPath).

MicrobeJ is an analysis platform specifically built for automated analysis of the most common intensity, morphological and spatiotemporal measurements from bacterial datasets. MicrobeJ enables customised detection of unique features, is optimised for high-throughput, and has a rich user interaction.

Collection of Fiji macros to automate the boring stuff: batch process all files in a folder and save them by converting from .czi images (Bioformats) to .tif format; save all open images in .tif format in an output folder of choice; batch process all .tif files in a folder and save 3 channels separately; apply local contrast enhancement (CLAHE) to a Z-stack; batch segmentation of cell nuclei (or other blob-like objects) in fluorescence images by auto-thresholding.