Repository Index

A curated list of awesome cytodata resources https://www.cytodata.org/awesome-cytodata/

• awesome-list
• awesome
• image-analysis
• morphology

Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy

• biology
• fluorescence
• image-analysis
• image-processing

NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

• r
• neuroanatomy-toolbox
• cran
• neuron

:art: Image processing toolbox for R

• r
• bioinformatics
• image-processing
• image-analysis

Tool for segmentation in bioimaging

• napari
• bioimage-analysis

A foundation model-driven whole slide image-scale cell phenotyping method with QuPath integration Resources

• bioimage-analysis
• cell-classification
• computer-vision
• digital-pathology

HistoClean is a tool for the preprocessing and augmentation of images used in deep learning models. This easy to use application brings together the most popular image processing packages from across the python universe, meaning no more looking at documentation! HistoClean provides real time feedback to augmentations and preprocessing options. This allows users to evaluate their steps before implementation.

• image-processing
• images
• image-analysis
• deep-learning

Plugins for bone image analysis

• fiji-plugin
• image-analysis
• image-processing
• imagej-plugins

Lattice light-sheet post-processing utility.

• microscopy
• light-sheet
• image-processing
• image-analysis

Imagej macro to calculate the MTF based on a knife edge measurement

• imagej-macro
• electron-microscopy
• image-analysis
• x-ray-imaging

Modular image and object analysis workflows for ImageJ/Fiji

• fiji-plugin
• modular
• imagej
• image-processing

🔬Python package for high-throughput single-cell imaging analysis.

• microscopy-image-analysis
• single-cell-analysis