I have a big but simple set of segmented 2D TEM data - traced arealists of mitochondria and endoplasmic reticulum.
I have already sorted out the analysis of the exported arealist masks separately in python. However, I need to export some 300+ traces from TrakEM2 as tiff files for further processing and I want to stay organized (ie., retain the template architecture and blind-identifiers of the images/ROIs).
What I would like to do is export mitochondria arealists as “/-.tiff” (eg. “740/740-m1.tiff”), and ER traces as “/--ER.tiff” (eg. “740/740-m1-ER.tiff”).
I have been looking through the scripting examples, but haven’t quite figured out how to navigate the template tree and pull out the right information and traces for export.
Below I have uploaded a screenshot of my template with a sample of the objects and layers. To be clear, this is all 2D analysis, with layer/object names corresponding to blinded identifiers for the analyzed images.
Please let me know if any of you have any more resources or ideas for scripting beyond - really any help and feedback would be appreciated.