Repository Index

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

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

python functions for simulating optical transfer functions

• microscopy
• numpy

Minerva Story is an image viewer that is designed specifically to make it easy for non-expert users to interact with complex tissue images.

• minerva
• microscopy
• ome
• immunofluorescence

Gaussian processes and Bayesian optimization for images and hyperspectral data

• image-processing
• hyperspectral-images
• gaussian-processes
• bayesian-optimization

Methods for Image-Based Cell Profiling

• profiling
• microscopy
• r

Pure Python library for reading NIS Elements ND2 images and metadata

• nd2
• pims
• nikon
• nis-elements

ZetaStitcher is a tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.

• stitching
• microscopy
• microscopy-images
• fluorescence-microscopy-imaging

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

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

Lattice light-sheet post-processing utility.

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

Noise Correction Algorithm for sCMOS cameras

• cmos
• imaging
• noise
• readout

Single-cell fluorescence microscopy data analysis

• microscopy
• fluorescence-microscopy-imaging

An interactive image processing program for biologists written in Python.

• biologists
• python
• imagej
• calcium

Z-stack Depth Colorcode ImageJ FIJI plugin

• imagej-plugin
• colorcode
• fiji
• imagej

Accurate segmentation of bacterial microscope images using deep learning synthetically generated image data.

• microscopy
• image-processing
• segmentation
• biology

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

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

Fiji/ImageJ macros to quickly add a scale bar to an (electron microscopy) image.

• imagej
• fiji
• electron-microscopy
• scalebar

A python package to analyze the matrix fiber orientation and intensity around cells in fiber matrices (as a proxy for cellular forces).

• imaging
• microscopy
• contractility
• collagen

#ZVQ - Zebrafish Vascular Quantification - https://doi.org/10.1242/dev.199720

• segmentation
• image-processing
• zebrafish
• vasculature

[DEPRECATED] A package for storing morphological profiling data.

• profiling
• microscopy
• database

DetecDiv provides a comprehensive set of tools to analyze time microscopy images using deep learning methods. The software structure is such that data can be processed either at the command line or using a graphical user-interface. Detecdiv classification models include : image classification and regression, semantic segmentation, LSTM networks to analyze data and image timeseries.

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

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

Panoptic segmentation algorithms for 2D and 3D electron microscopy images

• deep-learning
• semantic-segmentation
• segmentation
• pytorch

Python library for statistical analysis of mRNA and protein distributions in fluorescent microscopy images