Bioimage informatics

Synonyms
Bioimage analysis
Description

TGMM is a cell tracking solution for large 3D volume (typically lightsheet).

It detects cell nuclei by fitting gaussians on their fluorescent intensity.

It can run on GPU using CUDA and is called via the command line.

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Description

Starting from image stacks, the nuclear boundary as well as nuclear bodies are segmented. As output, NucleusJ automatically measures 15 parameters quantifying shape and size of nuclei as well as intra-nuclear objects and the positioning of the objects within the nuclear volume.

has function
Description

Summary

napari is a fast, interactive, multi-dimensional image viewer for Python. It’s designed for browsing, annotating, and analyzing large multi-dimensional images. It’s built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (e.g. numpyscipy). It includes critical viewer features out-of-the-box, such as support for large multi-dimensional data, and layering and annotation. By integrating closely with the Python ecosystem, napari can be easily coupled to leading machine learning and image analysis tools (e.g. scikit-imagescikit-learnTensorFlowPyTorch), enabling more user-friendly automated analysis.

Installation

  • The installation procedure for Silicon Mac (M1 Processor, arm64 ) requires some tricks. As of Oct 2021, this procedure by Peter Sobolewski works but:
    • For installing pyqt5, use a slightly different command `brew install PyQt@5` to install PyQt5.  

 

Description

Wavelet Toolbox™ provides apps and functions for the time-frequency analysis of signals and multiscale analysis of images.

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Description

ASAP allows to automatically detect, classify and quantify structures acquired by super resolution microscopy.