Resources for Microscopy Image Analysis - Microlist

Techniques

Image Analysis

Image Analysis Forum: image.sc

The image analysis discussion forum

QuPath Training Course: From Samples To Knowledge

Format: In-person
Starts on 2023-10-09
Location: San Diego, CA, USA, 32.71574, -117.16108

Quantitative BioImaging Workshop on Multiplex Image Analysis

Format: Hybrid (in-person & remote options)
Starts on 2023-10-12

SIPAIM Conference

Format: In-person
Starts on 2023-11-15
Location: Mexico City, CDMX, Mexico, 19.43261, -99.13321

Video tutorial - dual-axis tomogram generation in Etomo (IMOD)

Video tutorial on dual-axis tomogram generation in eTomo

Seeing is believing: imaging the molecular processes of life

Format: Hybrid (in-person & remote options)
Starts on 2023-10-04
Location: Heidelberg, Germany, 49.39875, 8.67243

Bioimage Data Analysis Workflows ‒ Advanced Components and Methods

Desigingn and implementing bioimage analysis workflows

amsikking: Microscope objectives

A guide to objective lens properties

Dragonfly (Non-Commercial Licensing)

Non-commercial license for Dragonfly software
Licensed by Object Research Systems

Microscopy Image Browser

MATLAB-based software package for advanced image processing
Created by Ilya Belevich, Merja Joensuu, Darshan Kumar, Helena Vihinen and Eija Jokitalo

Weka

Data mining with open source machine learning software
Created by University of Waikato

Microscopic Image Analyzer (MIA)

A software for deep learning based image analysis
Created by Nils Körber

Bioimage Model Zoo

Advanced AI models in one-click

Open Source 3D Printed Microscope

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

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

Deep Learning Based Segmentation For Biologists

An online workshop

Bioimage Informatics Index

An extensive database of image analysis tools
Created by NEUBIAS

Image Analysis Methods for Biologists

A 4-week online course

Python Bioimage Computing Toolkit

Python functions, scripts, and classes
Created by Marcelo Cicconet

Image to Knowledge (I2K) Tutorials

Image analysis tutorials from I2K

Image Processing and Analysis for Life Scientists

A self-paced ~7 week online course

BioImage Analysis Workshop

5 session workshop on bioimage analysis

FIJI Image Processing and Analysis Workshop

PDF slides and reference list

BioImage analysis with Fiji/ImageJ

Introduction to Light and Fluorescence Microscopy by Sydney Microscopy and Microanalysis

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

SPIMagine

GPU accelerated volume rendering
Created by Weigert M

MyScope Training

Online microscopy learning environment

Mastodon

Tracking and track-editing framework

Advanced Cell Classifier

Machine learning method for image data analysis
Created by Horvath Lab

Nucleaizer.org

A cell segmentation tool
Created by Horvath Lab

CIDRE

A flatfield illumination correction method
Created by Horvath Lab

Napari

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

CSBDeep

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

AIDAhisto

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

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

FrapCalc

Analyzes FRAP curves with various models
Created by K Miura

easyFRAP

Quantitative and qualitative analysis of FRAP data
Created by Lygerou Lab

EAMNET Downloads

Links to Macros and software packages
Created by EAMNET

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

Multi-view reconstruction

Software for reconstruction of multiview images
Created by Preibisch Lab

BigStitcher

Stitching for large datasets
Created by Preibisch Lab

BioImage Archive

A hub for biological images
Created by EMBI-EBI

TOOL-AI

A blog about tools for image analysis

QuPath

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

pyCUDAdecon

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

Danuser Lab Software

Several different software packages available
Created by Danuser Lab, UTSW

Image Data Resource

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

Analyzing Fluorescence Microscopy Images with ImageJ

An online ImageJ textbook

Image Analysis with Fiji

Slides & test data

Pixel Chart

Learn how an image histogram is formed
Created by Andrei Kashcha

PatternUnmixer 2.0

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

CellOrganizer

Model learning tools
Created by Murphy Lab, Carnegie Mellon

ilastik

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

BioImageXD

Analyzing, processing & visualizing nD images

BisQue

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

Image Analysis Focused Interest Group

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

PSFj

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

FIJI

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

CellProfiler

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

Image and Data Analysis Core Software List

A list of open-source software for image analysis

Icy

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