Software and Databases

Image Analysis - Commercial Packages

Bitplane Imaris 3D Analysis

3D/4D image visualization and analysis

Download viewer and converter
Basic intro
Advanced use

Learning center
Download reference manual

SVI Huygens Deconvolution

High resolution image processing and deconvolution

Download temporary license
Basic intro
Various functions tutorials
Nyquist calculator
Download user guide

Olympus CellSens Image Analysis

Whole slide (slide scanner) image processing and analysis

Download OlyVIA viewer
Some tutorials

Other Viewers/Resources

Pipelines, image visualization, and simple processing/quantification

MetaXpress high content analysis webinars
Leica LASX: download LASX Core viewer
Nikon NIS Elements: download NIS-Elements viewer
Zeiss Zen: download Zen Lite viewer

Image Analysis - Open Source Software

ImageJ/Fiji Image Analysis

Java-based multidimensional image processing and analysis (NIH)

Download software
Basic intro
Advanced use: Scripting
Documentation page
Download user guide

Ilastik Machine Learning

Machine learning for image segmentation (Kreshuk lab, EMBL)

Download software
Recommended intro
Documentation page

CellProfiler Batch Analysis

Computer vision high-throughput image analysis (Carpenter lab, MIT/Harvard)

Download software
Basic intro
Pipeline examples
Download manuals

Icy BioImage Informatics

Plugins-based and graphical programming image analysis (BioImage Analysis Lab, Institut Pasteur / France-BioImaging)

Download software
Available protocols/plugins 

QuPath Digital Pathology

Whole slide object annotation, detection, classification, and analysis (University of Edinburgh)

Download software
Basic intro
List of tutorials
Documentation page
Recent workshop
 

Databases

SpectraViewer

Fluorescent probes spectral database

SpectraArizona

Fluorescent probes 1P/2P spectral database (University of Arizona)

FPbase

Fluorescent proteins properties database