Image WG Image Data Analysis and Management
Image Analysis Software

Foreword

Within this page, the GerBI-GMB Workgroup Image Data Analysis and Management provides an overview of selected (*) image analysis software packages. In addition, the advanced user might also find some deeper insights on the Bioimage Informatics Search Engine (BISE) web page which is supported by the Neubias Cost Action.

 

(*) We'd like to point out that this list represents only a small fraction of available software. The selection is based on criteria like:

  • Usability (for basic users)
  • Open Source software
  • Software which is mainly used by the community (based on the results of the German BioImaging Image Analysis Survey)
  • Software which is supported by a large (developer) community, thus providing sustainability
  • Exptertise/Focus of the Image Analysis Workgroup members

List of Software Packages

Software Package Category Example Tasks Appearance
Fiji | ImageJ
  • "Standard" Image Analysis
  • Interactive representations
  • counting nuclei & spots in 2D
  • Object tracking in 2D (2D + t tracking)
  • 3D object based co-localization
Image Fiji-Desktop
ilastik
  • Object classification
  • Image segmentation
  • 2D/3D tracking
  • Interactive representations
    • Counting nuclei & spots in 2D
    • Object tracking in 2D (2D + t tracking)
    Image ilastik-Desktop

     

    KNIME

    Data Pipelines

    • "Standard" & High-throughput Image Analysis
    • Interactive representations
    • Statistics /Data exporation
      • Counting nuclei in 2D
      • Analyzing cytoplasm intensity in 2D
      • Counting nuclei & spots in 2D
      Image Knime-Desktop

       

      CellProfiler

      Data Pipelines

      • High-throughput Image Analysis
      • Statistics
      • Segmenting and analysing objects
      Image CellProfiler-Desktop