Image analysis

BioImage Analysis - an integral part of your experiment

Acquiring good data is a prerequisite, but certainly not sufficient, for deriving meaningful information. At the KNIC facility we provide you not only with a high-end workstation and software, but also support with fitted image analysis, direct you to suitable methodologies, or point to specific optimization steps. 

Your data is influenced by:

  • Sample preparation (label choice)
  • Imaging modality (point scanning/ light sheet/ widefield)
  • Imaging parameters (bit depth/ dwell time/ pixel size/ source intensity
  • Analysis parameters (threshold)

Work efficiently:

  • Define your analysis - what are you aiming for?
    • Morphology/Intensity/Tracking/Colocalization
    • Sometimes you will need separate experiments
  • Acquire a minimal dataset
  • Manually verify your analysis makes sense before progressing!

Where to start?

Get familiar with sources:

Neubias, Network of European BioImage Analysts
Training/ Algorithms/ Database/ Community


  1. Segmentation of biological samples - Intro by Jonas Ogaard
  2. Bioimage data analysis - Edited by Kota Miura
  3. Analyzing fluorescence microscopy images with ImageJ - Peter Bankhead

Compare methodologies

Example: Objective comparison of particle tracking methods

"Oh no love, you're not alone"

There are many good algorithms and open source pipelines that can fit your needs- don’t rush into developing solutions that already exist! 
Check the forum, Biii and Quarep for questions.