CCI – Centre for Cell Imaging

Image Analyses Education

GENERAL:

Single stop resource Image analysis questions: https://forum.image.sc/

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

All about fluorescent proteins (by Tally Lambert, HMS): https://www.fpbase.org/

iBiology: microscopy courses: link

Neubias Academy: link

FIJI

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: https://github.com/wbif-bristol/ImageJ-Fiji-Level-2-course

Peter Bankhead FIJI image analysis github: https://petebankhead.gitbooks.io/imagej-intro/content/

3D viewing:

  1. https://www.youtube.com/watch?v=wgr82s0VBi4 (Daly, 20m)
  2. https://www.youtube.com/watch?v=OPC2kP-5By4 (Boudier, Neubias, 1 h 47 min)
  3. https://www.youtube.com/watch?v=i-Ta4vCRW2s (DelaCryz, 9 min, if you can stand the music)
  4. https://brcf.medicine.umich.edu/wp-content/uploads/2020/01/FIJI_QKSRT.pdf for FLuorender and FIJI instructions

Cell Profiler:

Tutorials at the Cell Profiler website (https://cellprofiler.org/tutorials)

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

ICY:

Marion Louveaux (2021):link

QuPath:

https://www.youtube.com/watch?v=4An5n6Y_rRI (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 (https://napari.org/)

Machine Learning:

IMJOY https://imjoy.io/#/

ZeroCost4Mic (https://www.nature.com/articles/s41467-021-22518-0)

Cellpose: https://www.cellpose.org/

Stardist: https://github.com/stardist/stardist, Martin Wiegert Neubias workshop video: link

WeKA: https://imagej.net/plugins/tws/, video: Anna Klem: link

Ilastik: https://www.ilastik.org/documentation/objects/objects

DeepImageJ: https://deepimagej.github.io/deepimagej/