Problems displaying large image files in trakem

We use SEM based STEM imaging for recording serial EM sections. Single images are up to 32k x 32k in size. Possibly because of the large image size we have several issues in trakem2.

We can import large stacks of such images and all images are nicely displayed at all desired resolutions. But after applying elastic registration, trakem has some difficulties. With mipmas enabled we can browse through all images at low magnification and everything seems fine. But if we zoom in to 100%, only one half of each image is displayed correctly, while the other half may be composed of several small tiles or just consist of some noise. The same pattern occurs already at low magnification, if we disable mipmaps.



Due to this problems we also cannot export flat images from a small subregion. The result shows the same errors as above. This may also occur if we want to export for CATMAID.

Interestingly, no problems occur, if we create subprojects of small ROIs. Even if we choose a region which is not correctly displayed in the main project, the subproject is displayed fine also at high resolution.

Nevertheless, it would be nice, if we could display also the main project correctly…

We tried it on different machines:

  • 64 cores, 256 GB RAM, Ubuntu 16.04, Fiji up to date

  • 32 cores, 128 GB RAM, Ubuntu 16.04, Fiji up to date

  • 8 cores, 96 GB RAM, Windows 10, Fiji up to date

We also played around with Java parameters related to heap management, but it did not change anything.

Does anybody have an idea how to fix these problems?