Big image data file formats

[tischi]

@bugraoezdemir @manerotoni

I think I would like to add a new module (in fact I think I need it for a course in two weeks).

Big image file formats

Concepts:

• Resolution pyramids
• Chunking

We have already this: https://neubias.github.io/training-resources/image_file_formats/index.html But I feel the above concepts justify a new module.

What do you think? Suggestions for module title?

[tischi]

Draft is here: https://neubias.github.io/training-resources/big_image_file_formats/index.html

[maulakhan]

• • naively (actually I did not get what a naive opening is)
• • implementations

General: concepts of lazy-loading, chunking and resolution pyramid are not explained

[maulakhan]

• Figure caption: Top row: resolution pyramids - Thick and thin lines show chunks and pixels respectively. Selected (chunks!?) are highlighted in yellow. Bottom row: Data display from selected chunks (actually I don't know myself, this is what I understood from image)

[maulakhan]

• do not

[bugraoezdemir]

@tischi As the module name, I would maybe suggest "Chunked data storage formats". Are you going to include an OME-Zarr example, too? It could be interesting to compare between TIFF, HDF5 and OME-Zarr.

[maulakhan]

• Check/set how much RAM Fiji is allowed to use by

  • Edit > Selection > Memory & Threads... and set the Maximum memory to a value to accommodate your data according to your system requirements if possible

• Question: Creating Orthogonal views is faster or browsing (zooming, panning, shifting slices etc.) them?