Hi all,
Its been a while I am trying to process the SBF-SEM data set for 3d reconstruction and am following a pipeline described by Pierre Magistretti. et. al (2019). The problem am facing is am unable to export arealists as labels (TIFF). Every time I try to export the area list the confirmation dialogue box pops up but the resulting labels window don’t show any arealist except the black image. I have tried exporting arealists as labels in v1.51s and v1.51p both.
Thank you all for your help.
I was having the same problem exporting arelists in TrakEM2. It seems as if the exported area are there in the stack but they are just very, very dark.
With the exported stack open, go to image > adjust > brightness/contrast and move the maximum brightness slider from 255 to 0. The areas from your arealist should now be visible. Then click apply > apply LUT to all images in stack. You should now have a usable stack for your 3D reconstruction.
Hope that helps.
hi @FungusAmungus,
You can also apply the GLASBEY LUT to the exported area list to easily visualize the cells or segmentations in the stack.
Hope it will save someone the misery of figuring it out.