How to deal with memory issues reading HCS plates

[tischi]

@ThomasMicroscopy

Also, how to deal with memory issues. A plate dataset can be quite large, more than RAM. For example, a 384 well plate, with 3x3 sites, and 3 wavelengths, is already >10'000 pictures. Not sure which dataset it was, but when I was moving around, zooming in and out on wells, eventually I got numerous
"Exception in thread "Fetcher - X" [X a number] java.lang.OurOfMemoryError: Java heap space.
It slowed down a lot, but I was still able to quit the program regularly.
Any tips how to deal with this?

[tischi]

I see two possibilities:

1. I could work on implementing a lazy resolution pyramid in MoBIE
2. The user, e.g. @ThomasMicroscopy, could convert their HCS data to a resolution pyramid OME-Zarr HCS using this converter tool

[tischi]

And, of course:

3. In Fiji: Edit › Options › Memory & Threads... and enter the highest number there that your computer supports.

[ThomasMicroscopy]

Thank you for the tips. Solution 1: Lots of work for you. Solution 2: if really needed, user can convert data.
Solution 3: Be aware of the limitation, don't zoom in and out wildly all over the plate.... ;-)

[ThomasMicroscopy]

yes, I will check the memory