Resources for Microscopy Image Analysis | Microlist

Techniques

Image Analysis

FIJI

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

Quantitative Imaging: From Acquisition to Analysis

14 days
in Cold Spring Harbor, NY
Applications due on 2020-01-31

12th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics

Begins 2019-10-19
in Suzhou, Jiangsu, China

Advanced Methods in Bioimage Analysis

6 days
in Heidelberg, Germany

Deep Learning for Image Analysis

5 days
in Heidelberg, Germany
Applications due on 2019-09-20

Network of European BioImage Analysts (NEUBIAS) Conference & Symposium

Begins 2020-02-29
in Bordeaux, France

TOOL-AI

A blog about tools for image analysis

Single Cell Data Analysis: Current Approaches and Challenges

Begins 2019-07-22
in London, UK

Image Processing Course

2 days
in London, UK

14th LFD Workshop in Advanced Fluorescence Imaging and Dynamics

5 days
in Irvine, CA
Applications due on 2019-09-20

From Pictures to Numbers

2 days
in University of Antwerp, Belgium
Applications due on 2019-06-01

BioImage Informatics 2019

in Seattle, WA, USA

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 2020-09-17
in Madison, WI, USA

Bioimage Data Analysis

Software overview and examples of image analysis

Society of Biomolecular Imaging and Informatics

Begins 2019-09-17
in Boston, MA, USA

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

Analyzing Fluorescence Microscopy Images with ImageJ

An online ImageJ textbook

Image Analysis with Fiji

Online Course

Pixel Chart

Created by Andrei Kashcha
Open source

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
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

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
Open source

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

Advanced Fluorescence Imaging Techniques

6 days
in Heidelberg, Germany

Icy

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