Nanomesh
Nanomesh: A Python workflow tool for generating meshes from image data - Published in JOSS (2022)
Cellocity
Cellocity: A Python package for analysis of confluent cell layer dynamics - Published in JOSS (2021)
Minerva
Minerva: a light-weight, narrative image browser for multiplexed tissue images - Published in JOSS (2020)
BrainGlobe Atlas API
BrainGlobe Atlas API: a common interface for neuroanatomical atlases - Published in JOSS (2020)
symbac
Accurate segmentation of bacterial microscope images using deep learning synthetically generated image data.
frc
frc is a Python package for computing the Fourier Ring Correlation (FRC) of images using DIPlib
pybasic-illumination-correction
Python implementation of the BaSiC shading correction method
mcmicro
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
exllsm-circuit-reconstruction
Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery
lls-core
Napari plugin for custom analysis and visualization of lattice lightsheet and Oblique Plane Microscopy data. The plugin is optimized for data from the Zeiss lattice lightsheet microscope.
nbomicroscopymetadataspecs
The 4DN + BINA Tiered System of Microscopy Metadata Guidelines was developed by the 4DN Imaging Standards Working Group in collaboration with the BINA Data Management and Quality Control Working Group (https://www.bioimagingna.org/qc-dm-wg) for documenting microscopy experiments and assessing the quality of image data.
DeconvOptim
A multi-dimensional, high performance deconvolution framework written in Julia Lang for CPUs and GPUs.
spatialvi
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
https://github.com/pycroscopy/atomai
Deep and Machine Learning for Microscopy
https://github.com/pycroscopy/pycroscopy
Scientific analysis of nanoscale materials imaging data
https://github.com/brainglobe/brainreg-napari
Automated 3D brain registration in napari with support for multiple species and atlases.
https://github.com/clesperanto/pyclesperanto_prototype
GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data
cytominer-database
[DEPRECATED] A package for storing morphological profiling data.
https://github.com/google-research/sofima
Scalable Optical Flow-based Image Montaging and Alignment
https://github.com/bencardoen/smlmvis
Superresolution visualization of 3D protein localization data from a range of microscopes
flowcatchr
A framework for tracking and analyzing flowing blood cells in time lapse microscopy images
https://github.com/bionanoimaging/bionanoimaging.github.io
Repository for hosting the website files
https://github.com/bmorris3/shampoo
An open source digital holographic microscopy toolkit in Python.
https://github.com/cytomining/cytominergallery
[Deprecated] A Gallery of Cytominer Vignettes
gutanalysistoolbox
Analysis and characterisation of cells within the gut wall using deep learning models. The current focus is on studying enteric neurons and enteric glia.
deeptrack
DeepTrack2 is a modular Python library for generating, manipulating, and analyzing image data pipelines for machine learning and experimental imaging.
https://github.com/ccmim/origami
MATLAB-based image analysis pipeline for extracting single-cell direction-variant shape features from fluorescence images of folding epithelial sheets.
ijlookupstorm
ImageJ 1.x implementation of a 3D real-time single molecule localization microscopy algorithm based on lookup tables
12
Try to observe with a microscope what is making an UV/Vis spectroscopy method fail
brainreg
Automated 3D brain registration with support for multiple species and atlases.
omega
Open Microscopy Environment inteGrated Analysis (OMEGA) is a cross-platform data management, analysis and visualization system, for particle tracking data with particular emphasis on results from viral and vesicular trafficking experiments.
microaligner
Image registration (alignment) software for large microscopy images
nematode-fecundity-computer-vision-counting
Automated C. elegans counting system using deep learning (YOLO models) for fecundity assays
https://github.com/cytomining/cytoplot
[Deprecated] Package for visualizing high-dimensional single-cell data
simulatedmicroscopy
Python package to create synthetic (fluorescence) microscopy images of (nano)particles and convolution with a point spread function
Colocalization
Colocalization metrics and distances for images or their sparse representations.
napari_svetlana
The aim of this plugin is to classify the output of a segmentation algorithm
https://github.com/cea-metrocarac/pyvsnr
A Python library for computing the VSNR in 2D images. It provides both CPU and GPU implementations.
imswitch
ImSwitch is a software solution in Python that aims at generalizing microscope control by providing a solution for flexible control of multiple microscope modalities.
