Knowledge base BioImage Analysis

Bioimage analysis is the process by which one extracts numerical data from scientific images. A large number of software packages, methods, algorithms are available and allow for diverse types of analysis. The webpage biii.eu is a search engine, where one can find tools and information related to analysis. 

NEUBIAS - the network of European Bioimage analysts: organises courses and conferences, provides funding, etc

Interesting read: 

Bioimage Data Analysis, 2016, edited by Kota Miura, Wiley. Open access text book about image analysis. 

Analyzing fluorescence microscopy images with Fiji, Peter Bankhaed, open access handbook to get started with ImageJ/Fiji 

Software packages

Free, open source and cross platform

• Fiji
  Distribution of ImageJ, including a bundle of plugins facilitating scientific image analysis. 
  
  
• ImageJ 
  Open platform for scientific image analysis 
  
  
• Cell Profiler and Cell Profiler analyst
  Software for measuring and analysing cell images. Cell profiler analyst provides an exploration and classification of large biological image sets. 

• Icy
  Open community platform for Bioimage informatics. Visualisation, annotation, and quantification of bio imaging data. 
  
  
• IMOD 
  tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections

Free versions of commercial software packages

• BioImageXD
  open-source image analysis software
  (cross platform)

• IrfanView
  image viewer for common file formats like *.tif and *.jpg, provides simple processing and batch conversion, slide show etc.
  (Windows only)
  
  
• Leica LAS X Lite
  free Leica software, can open *.lif and *.lei files, acquisition information are accessible
  (Windows only)
  
  
• Olympus FV Viewer
  free Olympus software, can open *.oib and *.oif files from Fluoview Confocals
  (Windows only)
  
  
• Zeiss ZEN Lite
  free version of Zeiss Zen software for viewing and processing images including *.lsm, *.czi formats
  (Windows only)