Resources for Microscopy Image Analysis - Microlist

Techniques

Image Analysis

Image Analysis Forum: image.sc

An image analysis discussion forum

Quantitative Imaging: From Acquisition to Analysis

14 days
in Cold Spring Harbor, NY

Bioimage Model Zoo

Advanced AI models in one-click
Open source

Open Source 3D Printed Microscope

PUMA 3D Printed Microscope
Created by Dr Paul J. Tadrous
Licensed by GPL v3.0
Open source

Global BioImaging Training Resource

Online Training Resource

Batch analysis and macro development in ImageJ/Fiji: going beyond the basics

3 days
in porto, Portugal
Applications due on 2021-10-15
Course starts on 2021-11-24

Crick BioImage Analysis Symposium 2021

Begins 2021-11-22
This event will take place online

Introduction to digital bioimage analysis

5 days
in Porto, Portugal
Course starts on 2021-10-12

BioImage Informatics 2021

Begins 2021-12-29
This event will take place online

Introduction to Modern Statistics

Free online textbook

Center for Open Bioimage Analysis YouTube Channel

CellProfiler tutorials

Python tutorials for image processing

Python tutorials for image processing

Quantitative Phase Microscopy Software interface

GPU DHM
Created by Lee Lab @JCSMR
Open source

Deep Learning Based Segmentation For Biologists

Online Course

Bioimage Informatics Index

An extensive database of image analysis tools
Created by NEUBIAS
Open source

Image Analysis Methods for Biologists

Online Course

Python Bioimage Computing Toolkit

Python functions, scripts, and classes
Created by Marcelo Cicconet
Open source

Image to Knowledge (I2K) Tutorials

Image analysis tutorials from I2K

Image Processing and Analysis for Life Scientists

Online Course

BioImage Analysis Workshop

Online Course

FIJI Image Processing and Analysis Workshop

Online Course

MaxBI Technical Training @ Home: Image Analysis

Online Course

BioImage analysis with Fiji/ImageJ

Introduction to Light and Fluorescence Microscopy

Free online theory lectures

Mesmerize: A highly versatile platform for calcium imaging analysis

Platform for Calcium imaging analysis
Created by Kushal Kolar, Daniel Dondorp, Marios Chatzigeorgiou
Open source

Trends in Microscopy / GerBI-GMB Spring School

5 days
in Münsingen, Germany
Course starts on 2022-03-21

SPIMagine

GPU accelerated volume rendering
Created by Weigert M
Open source

Mastodon

Tracking and track-editing framework
Open source

Advanced Cell Classifier

Machine learning method for image data analysis
Created by Horvath Lab
Open source

Nucleaizer.org

A cell segmentation tool
Created by Horvath Lab
Open source

CIDRE

A flatfield illumination correction method
Created by Horvath Lab
Open source

Napari

Fast ND image viewer for python
Created by Sofroniew, Royer, Nunez-Iglesias et al (doi:10.5281/zenodo.3555620)
Open source

CSBDeep

A toolbox for Content-aware Image Restoration (CARE)
Created by Weigert M et al
Open source

AIDAhisto

A tool optimised for quantification of histological staining of mouse brain tissue
Created by Niklas Pallast and Markus Aswendt
Open source

Python for Microscopist Videos

YouTube channel with educational videos on Python coding

Bioimage Analysis Course: Life cycle of an image data set

Graduate student level introduction to bioimage analysis

Image Tools Resource

List of open-source analysis software for bioimaging
Created by Image Data Resource
Open source

FrapCalc

Analyzes FRAP curves with various models
Created by K Miura
Open source

easyFRAP

Quantitative and qualitative analysis of FRAP data
Created by Lygerou Lab
Open source

EAMNET Downloads

Links to Macros and software packages
Created by EAMNET
Open source

BioImage Data Analysis

An open access text book on 'BioImage Data Analysis'

PyImageSearch

Object-recognition with Python/OpenCV

Multi-view simulation

Code for simulating a multiview acquisition
Created by Preibisch Lab
Open source

Multi-view reconstruction

Software for reconstruction of multiview images
Created by Preibisch Lab
Open source

BigStitcher

Stitching for large datasets
Created by Preibisch Lab
Open source

BioImage Archive

A hub for biological images
Created by EMBI-EBI
Open source

Deep Learning for Image Analysis

8 days
in Heidelberg, Germany
Online Course
Course starts on 2021-12-03

TOOL-AI

A blog about tools for image analysis

QuPath

software for whole slide image analysis
Created by Pete Bankhead and Jose Fernandez
Open source

Image to Knowledge (I2K): ImageJ User and Developer Conference

Begins 2022-05-09
This event will take place in-person
in Madison

pyCUDAdecon

Python wrapper for cudaDecon - 3D deconvolution
Created by Talley Lambert, Harvard Medical School
Open source

Danuser Lab Software

Several different software packages available
Created by Danuser Lab, UTSW
Open source

Image Data Resource

Online, public data repository
Created by University of Dundee & Open Microscopy Environment
Open source

Analyzing Fluorescence Microscopy Images with ImageJ

An online ImageJ textbook

Image Analysis with Fiji

Pixel Chart

Learn how an image histogram is formed
Created by Andrei Kashcha
Open source

PatternUnmixer 2.0

Object type recognition for automated analysis
Created by Murphy Lab, Carnegie Mellon
Open source

CellOrganizer

Model learning tools
Created by Murphy Lab, Carnegie Mellon
Open source

ilastik

Interactive learning and segmentation toolkit
Created by Anna Kreshuk's lab, EMBL
Open source

BioImageXD

Analyzing, processing & visualizing nD images
Open source

BisQue

Store, visualize, organize and analyze in the cloud
Created by UCSB Center for Bio-image Informatics
Open source

Image Analysis Focused Interest Group

Content to support the image analysis community
Created by Royal Microscopy Society
Open source

PSFj

Software for point spread function analysis
Created by Knop Lab, ZMBH
Open source

FIJI

ImageJ bundled with a lot of plugins
Created by Curtis Rueden & the ImageJ development team at LOCI, U. Wisconsin-Madison
Open source

CellProfiler

For measuring and analyzing cell images
Created by Carpenter Lab, Broad Institute
Open source

Image and Data Analysis Core Software List

A list of open-source software for image analysis
Open source

Icy

Platform for bioimage informatics
Created by Quantitative Image Analysis Unit, Institut Pasteur
Open source