Fiji from 0 to 100 in 5.5 ksecs...

You can find here four videos that take you from "where do I download Fiji?" to "I can use scripting to build pipelines for imageS processing".

1. Fiji technicalities (18 mins), 11 slides
2. Inspecting images in Fiji (26 mins)
3. Macro and Jython scripting (36 mins)
4. Pipelines building in Fiji (12 mins)

They are a bit rushing to fit in total into 92 mins. If you want to be trying things along, please, excercise the play-a-bit-pause-try-at-home-rewind-replay pattern.

The videos were postprocessed for noise suppression, and mainly to cut and shuffle at many places. The transitions are sometimes noticable, please excuse it.

Futher relevant material:

• Fiji homepage (and download)
• Fiji wiki - docs to major plugins
• The main Image processing and analysis forum
• Albert Cardona's excelent tutorial on Fiji Scripting
• GPU processing in Fiji
• Distributed (and parallel) processing in Fiji, 11 slides
• Tracking in Fiji with Mastodon
• Beyond Fiji: A Hitchhiker's guide through the bio-image analysis software universe

Hope it helps,
Vlado
[17th Dec 2022]

Feel free to reach me at ulman et fi.muni.cz

PS: The videos were recorded originally for the CEITEC CELLIM's workshop on Processing and Analysis of Boomedical Images: Focus on Lightsheet data