Orbit image analysis saving results

I am using Orbit image analysis software for cell segmentation (object detection). After training my model, classifying the whole image (large NDPI file) and performing segmentation, I now want to save the results. However, I cannot find the option to save the processed image (whole image including markup - that is annotations).

If I try the “Save full image” option it complains that the image is too large (only for images with width*height <= 8000*8000). It does mention that you can use the Orbit Agent to download the file, however I cannot find any information about this in the documentation.

Also, is there a way to save the processed / segmented image (maximum classification opacity) using better quality (for ex. .tiff)? The default image out of “Save Classification Image” is very low quality and doesn’t include the yellow boundaries.

Additionally, I see that there is an option to send your image to Cell Profiler under the Tools tab, is there such an option for ImageJ as well?

Hi there,

the general principle in Orbit is not to save results and just display them.
The idea behind is that if you really want to store overlays or segmentation masks you write a script which does it.

If Tools -> Save classification image has a too low resolution for you, you can run this script to save the classification image (set the width to a higher value of needed).

To store the segmentation outlines you can use this script which returns you a list of Shapes - then you can store them / draw them wherever you want.

Also you might have a look on this script from OME, there Will wrote a nice example how to store Orbit segmentations in OMERO.

And for imageJ - also therefore we have a script which runs an ImageJ macro per tile.

Hope that helps.

Regards,
Manuel