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.
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.
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.
MULTEM is a collection of routines written in C++ with CUDA to perform accurate and fast multi-slice simulations for different transmission electron microscopy experiments (such as HRTEM, STEM, ISTEM, ED, PED, CBED, ADF-TEM, ABF-HC, EFTEM and EELS).
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).
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.
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.
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.
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.
