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BIMSBbioinfo / VoltRon

Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration
http://bioinformatics.mdc-berlin.de/VoltRon/
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RBioformats Java Heap issue, and non-Java based dependancies for importing OME.TIFF images #114

Open NKalavros opened 1 month ago

NKalavros commented 1 month ago

Hi Artur,

Great work with this package! I was trying it today (Dev branch) for some of my Xenium data and noticed that I get a Java heap space issue.

I solved it using options(java.parameters = c("-XX:+UseConcMarkSweepGC", "-Xmx8192m")) before importing but is there some way it can be solved within the package?

Best, Nikolas

Artur-man commented 1 month ago

Much appreciated Nikolas :)

Yes, this is a problem that we are trying to work around at the moment.

RBioformats is the only Java-dependant dependancy we have in VoltRon at the moment and it requires these external configurations (I personally embedded this options(..) call in .Rprofile under home for default setting).

Please let me know if you also come up with an internal solution for this later. Another solution could be to use the BioFormats C++ wrapper for importing ome.tiff images, removing RBioFormats package dependancy all-together.

Best, Artür