CCI – Centre for Cell Imaging

Image Analyses Education


Single stop resource Image analysis questions:

Microcourses: Microscopy tutorials by Jennifer Waters (Harvard, HHMI/HMS): link

All about fluorescent proteins (by Tally Lambert, HMS):

iBiology: microscopy courses: link

Neubias Academy: link


Robert Haase: Bioimage analysis 2020 course: FIJI Python/Java: link Check out CLIJ as well.

Dominic Waithe 2020: FIJI intro – image processing explained: link

WBIF-bristol FIJI level2 course:

Peter Bankhead FIJI image analysis github:

3D viewing:

  1. (Daly, 20m)
  2. (Boudier, Neubias, 1 h 47 min)
  3. (DelaCryz, 9 min, if you can stand the music)
  4. for FLuorender and FIJI instructions

Cell Profiler:

Tutorials at the Cell Profiler website (

Elaborate intro: Nasim Jamali/Pearl Ryder I2K 2020: link

Example pipeline by Julia Sero (U. Bath) on nuc translocation pipeline: link

CellProfiler-Analyst Workshop Beth Cimini 2020: link


Marion Louveaux (2021):link

QuPath: (Peter Bankhead: Neubias Workshop 2021)

Python for image analyses:

RMS workshop python for bioimage analysis: link

DigitaSreeni python and filter explanations: link

THE viewer: Napari (

Machine Learning:


ZeroCost4Mic (


Stardist:, Martin Wiegert Neubias workshop video: link

WeKA:, video: Anna Klem: link