Projects in Awesome Lists tagged with microscopy

https://github.com/BMIRDS/deepslide

Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.

cancer histopathology-images lung medical-image-analysis microscopy pathology-image resnet sliding-windows wsi

Last synced: 07 May 2025

https://github.com/rapidsai/cucim

cuCIM - RAPIDS GPU-accelerated image processing library

computer-vision cuda digital-pathology gpu image-analysis image-data image-processing medical-imaging microscopy multidimensional-image-processing nvidia segmentation

Last synced: 11 Apr 2025

https://github.com/dana-farber-aios/pathml

Tools for computational pathology

biomedical-image-processing computational-pathology deep-learning digital-pathology fluorescence-microscopy-imaging histopathology image-analysis machine-learning microscopy pathml pathology python pytorch research spatial-transcriptomics

Last synced: 16 Sep 2025

https://github.com/Dana-Farber-AIOS/pathml

Tools for computational pathology

biomedical-image-processing computational-pathology deep-learning digital-pathology fluorescence-microscopy-imaging histopathology image-analysis machine-learning microscopy pathml pathology python pytorch research spatial-transcriptomics

Last synced: 06 May 2025

https://github.com/TIO-IKIM/CellViT

CellViT: Vision Transformers for Precise Cell Segmentation and Classification

ai cell digitalpathology microscopy ml python pytorch

Last synced: 06 May 2025

https://github.com/tio-ikim/cellvit

CellViT: Vision Transformers for Precise Cell Segmentation and Classification

ai cell digitalpathology microscopy ml python pytorch

Last synced: 12 Apr 2025

https://github.com/pycroscopy/pycroscopy

Scientific analysis of nanoscale materials imaging data

afm atom atomic-force-microscopy electron-microscopy fft imaging infrared machine-learning materials-science microscopy raman scanning scanning-probe-microscopy scanning-tunnelling-microscopy signal-processing spectroscopy statistics stem stm visualization

Last synced: 15 May 2025

https://github.com/clesperanto/pyclesperanto_prototype

GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data

bioimage-analysis gpu-acceleration microscopy

Last synced: 21 Oct 2025

https://github.com/brainglobe/cellfinder

Automated 3D cell detection in very large images

cell-detection deep-learning image-analysis imaging microscopy neuroanatomy neuroscience python

Last synced: 02 Feb 2026

https://github.com/clEsperanto/pyclesperanto_prototype

GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data

bioimage-analysis gpu-acceleration microscopy

Last synced: 21 Mar 2025

https://github.com/AllenCellModeling/aicsimageio

Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python

bio-formats dask image-metadata imageio microscopy python scientific-computing scientific-formats xarray

Last synced: 07 May 2025

https://github.com/allencellmodeling/aicsimageio

Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python

bio-formats dask image-metadata imageio microscopy python scientific-computing scientific-formats xarray

Last synced: 14 Apr 2025

https://github.com/pycroscopy/atomai

Deep and Machine Learning for Microscopy

deep-kernel-learning deep-learning electron-microscopy ensemble-learning fully-convolutional-networks google-colaboratory imaging jupyter-notebook machine-learning materials materials-science microscopy multivariate-analysis pytorch scanning-probe-microscopy semantic-segmentation variational-autoencoders

Last synced: 04 Apr 2025

https://github.com/brainglobe/brainglobe-atlasapi

A Python interface to access neuroanatomical atlases

atlases brain microscopy neuroscience python registration visualisation

Last synced: 18 Jun 2026

https://github.com/zudi-lin/pytorch_connectomics

PyTorch Connectomics: segmentation toolbox for EM connectomics

biomedical-image-processing computer-vision connectomics deep-learning microscopy neuroscience pytorch segmentation

Last synced: 01 May 2025

https://github.com/seung-lab/cloud-volume

Read and write Neuroglancer datasets programmatically.

big-data biomedical-image-processing chunked-image cloud connectomics electron-microscopy gcs large-image matrix mesh microscopy microscopy-images neuroglancer numpy python s3 serverless skeletons tensor volumetric-data

Last synced: 15 May 2025

https://github.com/brainglobe/brainreg

Automated 3D brain registration with support for multiple species and atlases.

atlases brain microscopy neuroanatomy neuroscience registration

Last synced: 17 Mar 2026

https://github.com/zeiss-microscopy/OAD

Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools and AI tools.

acquisition automation image-analysis image-processing imaging machine-learning microscopy oad open-source python python-script scripting workflow zen zen-blue

Last synced: 07 May 2025

https://github.com/jungmannlab/picasso

A collection of tools for painting super-resolution images

dna-paint microscopy smlm super-resolution

Last synced: 12 Jan 2026

https://github.com/cytomining/pycytominer

Python package for processing image-based profiling data

carpenter-lab cellprofiler cytominer image-processing microscopy morphological-profiling python way-lab

Last synced: 07 Jan 2026

https://github.com/axondeepseg/axondeepseg

Axon/Myelin segmentation using Deep Learning

axon convolutional-neural-networks deep-learning electron-microscopy histology machine-learning microscopy myelin neuropoly segmentation spinalcord

Last synced: 04 Apr 2026

https://github.com/aafkegros/MicroscopyNodes

Loading and handling microscopy data in blender

blender blender-addon microscopy volume-rendering

Last synced: 26 Oct 2025

https://github.com/turagalab/decode

This is the official implementation of our publication "Deep learning enables fast and dense single-molecule localization with high accuracy" (Nature Methods)

deep-learning gpu high-density localization-microscopy microscopy pytorch smlm

Last synced: 08 Apr 2026

https://github.com/TuragaLab/DECODE

This is the official implementation of our publication "Deep learning enables fast and dense single-molecule localization with high accuracy" (Nature Methods)

deep-learning gpu high-density localization-microscopy microscopy pytorch smlm

Last synced: 07 May 2025

https://github.com/dancsalo/tensorflow-mil

TF Implementation of Multiple Instance Learning FCN.

deep-neural-networks microscopy multiple-instance tensorflow

Last synced: 14 Apr 2025

https://github.com/weisongzhao/sparse-sim

Official MATLAB implementation of the "Sparse deconvolution" -v1.0.3

deconvolution fluorescence-microscopy-imaging image-processing image-restoration matlab-gui microscopy super-resolution

Last synced: 13 Apr 2025

https://github.com/david-hoffman/pyotf

python functions for simulating optical transfer functions

microscopy numpy

Last synced: 21 Feb 2026

https://github.com/royerlab/cytoself

Self-supervised models for encoding protein localization patterns from microscopy images

autoencoder deep-learning fluorescence imaging microscopy opencell protein pytorch self-supervised self-supervised-learning tensorflow

Last synced: 03 Jul 2025

https://github.com/pymmcore-plus/napari-micromanager

GUI interface between napari and micromanager powered by pymmcore-plus and pymmcore-widgets

micro-manager microscopy napari python

Last synced: 21 Feb 2026

https://github.com/matthewfilipovich/torchoptics

Differentiable wave optics simulation library built on PyTorch

computational-optics deep-learning differentiable-optics diffraction fourier-optics holography imaging inverse-design machine-learning microscopy optical-neural-network optics physics pytorch wave-optics

Last synced: 26 Oct 2025

https://github.com/PlanktoScope/PlanktoScope

Open and Affordable Quantitative Imaging Platform

citizen citizen-science imaging microscope microscope-platform microscopy ocean oceanography plankton planktoscope raspberry-pi-4 raspberry-pi-camera science water

Last synced: 07 May 2025

https://github.com/fairscope/PlanktoScope

Open and Affordable Quantitative Imaging Platform

citizen citizen-science imaging microscope microscope-platform microscopy ocean oceanography plankton planktoscope raspberry-pi-4 raspberry-pi-camera science water

Last synced: 03 Apr 2026

https://github.com/google-research/sofima

Scalable Optical Flow-based Image Montaging and Alignment

2d 3d 4d alignment-algorithm biomedical-image-processing connectomics electron-microscopy jax microscopy python3 stitching-algorithm

Last synced: 05 Apr 2025

https://github.com/tlambert03/fpbase

The Fluorescent Protein Database

database fluorescence microscopy

Last synced: 09 Apr 2025

https://github.com/roflmaostc/deconvoptim.jl

A multi-dimensional, high performance deconvolution framework written in Julia Lang for CPUs and GPUs.

deconvolution gpu image-processing julia microscopy

Last synced: 07 Mar 2026

https://github.com/tlambert03/nd2

Full-featured nd2 (Nikon NIS Elements) file reader for python. Outputs to numpy, dask, and xarray. Exhaustive metadata extraction

microscopy nd2 nikon nis-elements

Last synced: 08 Jan 2026

https://github.com/recursionpharma/maes_microscopy

Official repo for Recursion's accepted spotlight paper at NeurIPS 2023 Generative AI & Biology workshop.

biology computer-vision deep-learning generative-ai masked-autoencoder microscopy phenomics

Last synced: 06 Feb 2026

https://github.com/ziatdinovmax/GPim

Gaussian processes and Bayesian optimization for images and hyperspectral data

bayesian-optimization colab-notebook gaussian-processes hyperspectral-images image-processing lattice-models microscopy

Last synced: 07 May 2025

https://github.com/fideus-labs/ngff-zarr

A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.

dask imaging medical microscopy ome-zarr ome-zarr-converter python

Last synced: 16 Apr 2026

https://github.com/labsyspharm/minerva-story

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

immunofluorescence microscopy minerva ome

Last synced: 12 Feb 2026

https://github.com/biomedical-imaging-group/deconvolutionlab2

Java (ImageJ/Fiji) software package for 3D deconvolution microscopy

3d algorithms deconvolution images-plugins microscopy

Last synced: 06 Apr 2025

https://github.com/ziatdinovmax/gpim

Gaussian processes and Bayesian optimization for images and hyperspectral data

bayesian-optimization colab-notebook gaussian-processes hyperspectral-images image-processing lattice-models microscopy

Last synced: 14 Apr 2025

https://github.com/saeyslab/harpy

Single-cell spatial omics analysis that makes you happy!

analysis-framework bioinformatics hpc machine-learning microscopy napari-plugin spatial

Last synced: 17 Apr 2026

https://github.com/weisongzhao/sparse-deconv-py

Official Python implementation of the 'Sparse deconvolution'-v0.3.0

fluorescence-microscopy-imaging image-processing image-restoration microscopy python3 super-resolution

Last synced: 13 Apr 2025

https://github.com/tlambert03/ome-types

native Python dataclasses for the OME data model

metadata microscopy ome

Last synced: 04 Apr 2025

https://github.com/henriqueslab/nanoj-fluidics

Manual, source-code and binaries for the NanoJ-Fluidics project

automation dna-paint electronics fluidics high-content lego live-cell microscopy pump storm super-resolution

Last synced: 15 Sep 2025

https://github.com/tlambert03/psfmodels

Python bindings for scalar and vectorial models of the 3D microscope point spread function.

microscopy psf

Last synced: 11 Sep 2025

https://github.com/open-science-tools/nd2reader

Pure Python library for reading NIS Elements ND2 images and metadata

microscopy microscopy-images nd2 nikon nis-elements pims

Last synced: 12 Dec 2025

https://github.com/Open-Science-Tools/nd2reader

Pure Python library for reading NIS Elements ND2 images and metadata

microscopy microscopy-images nd2 nikon nis-elements pims

Last synced: 07 May 2025

https://github.com/pymmcore-plus/pymmcore-plus

Pure python/C++ micro-manager ecosystem

micro-manager microscopy ome-zarr python

Last synced: 03 Mar 2026

https://github.com/katrinleinweber/phd-thesis

Experimental tech-demo for PhD thesis in Scientific Markdown; official:

biochemistry biofilm biology citer diatom eds electron-microscopy latex latex-document latexmk make makefile markdown markdown-template microscopy pandoc phd-thesis zotero

Last synced: 29 Jul 2025

https://github.com/katrinleinweber/PhD-thesis

Experimental tech-demo for PhD thesis in Scientific Markdown; official:

biochemistry biofilm biology citer diatom eds electron-microscopy latex latex-document latexmk make makefile markdown markdown-template microscopy pandoc phd-thesis zotero

Last synced: 21 Jul 2025

https://github.com/lens-biophotonics/ZetaStitcher

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

fluorescence-microscopy-imaging microscopy microscopy-images stitching volumetric-images

Last synced: 07 May 2025

https://github.com/delmic/odemis

Open Delmic Microscope Software

microscopy python

Last synced: 27 Mar 2025

https://github.com/afermg/cp_measure

Morphological features from images and masks made easy.

computer-vision data-science imaging microscopy

Last synced: 14 Jan 2026

https://github.com/aelefebv/nellie

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

biology fluorescence image-analysis image-processing machine-learning microscopy organelles segmentation tracking

Last synced: 11 Mar 2025

https://github.com/AllenCellModeling/napari-aicsimageio

Multiple file format reading directly into napari using pure Python

imageio microscopy napari

Last synced: 07 May 2025

https://github.com/allencellmodeling/napari-aicsimageio

Multiple file format reading directly into napari using pure Python

imageio microscopy napari

Last synced: 14 Apr 2025

https://github.com/thewtex/ngff-zarr

A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.

dask imaging medical microscopy ome-zarr ome-zarr-converter python

Last synced: 07 Apr 2025

https://github.com/HuanglabPurdue/NCS

Noise Correction Algorithm for sCMOS cameras

algorithm cmos imaging microscopy noise noise-correction readout scmos super-resolution

Last synced: 07 May 2025

https://github.com/tlambert03/LLSpy

Lattice light-sheet post-processing utility.

image-analysis image-processing light-sheet microscopy

Last synced: 07 May 2025

https://github.com/mviereck/microscopy-tools

Tools for microscopic captures and focus stackshots (beta)

alignment arduino camera camera-configuration camera-control enfuse focus-stackshots fuse-stackshot-images imagemagick micrometer microscopy stacking stackshot stepper-motor tethered-shooting

Last synced: 11 Jul 2025

https://github.com/tlambert03/llspy

Lattice light-sheet post-processing utility.

image-analysis image-processing light-sheet microscopy

Last synced: 24 Aug 2025

https://github.com/hahnec/rf-ulm

RF-ULM: Ultrasound Localization Microscopy Learned from Radio-Frequency Wavefronts

ceus contrast-enhancement deep-learning imaging localization medical medical-imaging microbubble microscopy neural-network pytorch ulm ultrasound vascular vascular-flow

Last synced: 31 Jul 2025

https://github.com/13hannes11/focus_annotator

This is a tool to annotate the focus plane of z-stacked images.

adwaita data-annotation focus-stacking gtk4 gtk4-rs libadwaita microscopy rust wholeslide-imaging z-stack

Last synced: 21 Nov 2025

https://github.com/jhsmit/colicoords

Single-cell fluorescence microscopy data analysis

fluorescence-microscopy-imaging microscopy

Last synced: 14 Apr 2025

https://github.com/Jhsmit/ColiCoords

Single-cell fluorescence microscopy data analysis

fluorescence-microscopy-imaging microscopy

Last synced: 07 May 2025

https://github.com/allencellmodeling/actk

Automated Cell Toolkit

biology cell-biology image-processing microscopy pipeline

Last synced: 30 Apr 2025

https://github.com/tferr/scripts

:microscope::cocktail: Home of the ImageJ BAR: A collection of Broadly Applicable Routines for ImageJ

beanshell clojure groovy ijm image-analysis imagej imagej2 java jython microscopy python ruby scientific-workflows scripts-collection

Last synced: 14 Apr 2025

https://github.com/flika-org/flika

An interactive image processing program for biologists written in Python.

astrocytes biologists calcium fluorescence image-processing imagej microscopy neurons python

Last synced: 07 May 2025

https://github.com/janeliascicomp/vvdviewer

3D/4D volumetric rendering of microscopy data

microscopy neuroscience rendering vvd-viewer

Last synced: 24 Oct 2025

https://github.com/bmorris3/shampoo

An open source digital holographic microscopy toolkit in Python.

holography microscopy numerical-reconstruction open-source python

Last synced: 29 Jan 2026

https://github.com/UU-cellbiology/ZstackDepthColorCode

Z-stack Depth Colorcode ImageJ FIJI plugin

colorcode fiji fiji-plugin imagej imagej-plugin microscopy utrecht-university

Last synced: 07 May 2025

https://github.com/schornacklabslcu/amfinder

The Automatic Mycorrhiza Finder (AMFinder) allows for automatic computer vision-based identification and quantification of AM fungal colonisation and intraradical hyphal structures on ink-stained root images using convolutional neural networks.

deep-learning gtk2 image-analysis keras microscopy mycorrhiza neural-networks ocaml python3

Last synced: 12 May 2025

https://github.com/pymmcore-plus/useq-schema

An implementation agnostic schema for describing a sequence of events during a multi-dimensional imaging acquisition.

image-acquisition microscopy schema

Last synced: 01 Apr 2026

https://github.com/pymmcore-plus/pymmcore-widgets

A set of Qt-based widgets onto the pymmcore-plus model

gui micro-manager microscopy python

Last synced: 21 Feb 2026

https://github.com/brainglobe/cellfinder-core

Standalone cellfinder cell detection algorithm

cell-detection cellfinder image-analysis keras microscopy object-detection resnet tensorflow

Last synced: 29 Sep 2025

https://github.com/JaneliaSciComp/VVDViewer

3D/4D volumetric rendering of microscopy data

microscopy neuroscience rendering vvd-viewer

Last synced: 16 Apr 2025

https://github.com/biologytools/bioimager

A .NET microscopy imaging application based on Bio library. Supports various microscopes by using imported libraries & GUI automation. Supports XInput game controllers to move stage, take images, run ImageJ macros on images or Bio C# scripts.

histology image-acquisition image-stacks imagej imagej-macro imaging micro-manager microscope microscope-control microscope-stage-controller microscopy plugin scripting whole-slide-imaging

Last synced: 28 Feb 2026

https://github.com/georgeoshardo/SyMBac

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

biology deep-learning image-processing machine-learning microscopy segmentation synthetic-biology synthetic-data synthetic-dataset-generation

Last synced: 07 May 2025

https://github.com/mikehugheskent/pyholoscope

Optimised python package for digital holographic microscopy, both inline and off-axis, with GPU support.

gpu holography imaging inline microscopy off-axis optics

Last synced: 08 Apr 2026

https://github.com/sebi06/czitools

This repository provides a collection of tools to simplify reading CZI (Carl Zeiss Image) pixel and metadata in Python. In addition it also contains other useful utilities to visualize CZI images inside Napari.

czi image-processing microscopy python

Last synced: 09 Apr 2026

https://github.com/WolframResearch/BioFormatsLink

Package for interacting with Bio-Formats library in the Wolfram Language

bio-formats java jlink library mathematica microscopy wolfram-language

Last synced: 08 Jul 2025

https://github.com/wolframresearch/bioformatslink

Package for interacting with Bio-Formats library in the Wolfram Language

bio-formats java jlink library mathematica microscopy wolfram-language

Last synced: 10 Apr 2025

https://github.com/theislab/geome

anndata graph-learning microscopy pytorch-geometric

Last synced: 11 Oct 2025

https://github.com/brainglobe/brainreg-napari

Automated 3D brain registration in napari with support for multiple species and atlases.

anatomy atlases brain microscopy napari neuroscience registration

Last synced: 07 May 2025

https://github.com/ekatrukha/CurveTrace

Curve tracing ImageJ plugin

curve-tracing fiji-plugin imagej-plugins microscopy

Last synced: 31 Oct 2025

https://github.com/janeliascicomp/exllsm-circuit-reconstruction

Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery

image-processing lightsheet machine-learning microscopy neuroscience nextflow-pipelines pipeline segmentation

Last synced: 25 Jan 2026

https://github.com/biologytools/biogtk

A cross platform version of Bio library & program. Bio is a library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.

bio-formats biology cross-platform geojson gtk image-stacks imagej imagej-roi imagej-tiff microscopy omero openslide plugins qupath roi sam-2 segment-anything segment-anything-model whole-slide-image

Last synced: 15 May 2025

https://github.com/natearnas/bead-analyzer

An open-source tool for characterizing PSF and FWHM measurements from light-microscopic 2D and 3D images of microspheres.

microscopy microscopy-image-analysis

Last synced: 03 Apr 2026

https://github.com/cryoem-uoft/cryosparc2_public

CryoSPARC is the state-of-the-art platform used globally for obtaining 3D structural information from single particle cryo-EM data. The cryoSPARC platform enables automated, high quality and high-throughput structure discovery of proteins, viruses and molecular complexes for research and drug discovery.

cryo-em high-performance-computing image-processing microscopy molecular-biology

Last synced: 18 Sep 2025