Orbit memory settings

Dear all,
I got several questions regarding memory issues / how to set memory parameters in Orbit.
Here I try to give a short overview about it.

In general, Orbit caches image tiles and the more memory is has, the more tiles it can cache, thus the faster it is.
If you are using the Jar distribution and run Orbit from command line, simply adjust the -Xmx parameter, e.g. set -Xmx10g to give Orbit 10gb memory. It is recommend to use around 75% of your system memory.
In the status-bar you can see how much memory Orbit can use.

For other distributions it depends:

  • Linux:
    Orbit uses the JWM default settings. To use more/less RAM please modify /opt/orbit/orbit.sh script and enter e.g. -Xmx10g to give Orbit 10 GB of RAM.
    If you did not install Orbit under /opt/orbit then you probably start it via orbit-start.sh inside the Orbit folder. There you can att the -Xmx parameter, too.

  • Mac:
    By default Orbit uses max 5GB of RAM. If you have more, you can modify the file OrbitImageAnalysis-xxx.app/Contents/Info.plist and set the -Xmx5G to a higher value (e.g. 75% of your total RAM).

  • Windows:
    Orbit uses around 75% of your system RAM.

    If you want other settings you have to start it via java -jar from command line, e.g. cd into the /lib folder and start Orbit via
    java -Xmx10g -XX:MaxPermSize=150m -Djavax.xml.parsers.DocumentBuilderFactory=com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderFactoryImpl -cp “*” com.actelion.research.orbit.imageAnalysis.components.OrbitImageAnalysis

Hope that helps!

Cheers,
Manuel

Dear Manuel

First of all, many thanks for your amazing analysis program. I am starting to get into it.
I noticed that there is a serious memory leakage. Every time when you click the button “Classify” under “Classification”, the program take up new memory without releasing the old memory. Could you please have a look at it?

Another problem that I have is when opening tiff or leica file. The program will be really really slow when you move within the image from one point to another. It take up to 20 seconds to move. When I converted the tiff file into jpg file. It seemed to be much better. But it could be because the jpg file just has smaller size compared to the original tiff file.

Cheers,
Tony

Dear Tony,

thanks a lot for using Orbit and reporting this issue.
Actually Orbit (Java) uses as much memory as you allow Orbit to use (so until the memory-bar in the status-bar is “full”) and first then starts to clean up memory.
This is ok, it just looks a bit strange because people are assuming there’s a memory problem.

Your second issue seems to be something more serious. Probably there’s a missing image pyramid in the image. Actually Tiff can mean many things - it’s a container and the content is not standardized (as long as it’s not e.g. ome-tiff). If the tiff contains an image pyramid Orbit recognizes it and then it should be fast.
What is you original image format - an svs?

Regards,
Manuel