I am having a issue when trying to import/save TIFF data in a way that lets me add the scaling information. I have a single file ImageJ hyperstack .tiff that has my entire volume, with X-Y scale of 0.001282 microns/pixel and a Z-step size of 0.000641 microns. When I initially loaded it using add data, it opens without any issues, and I can easily scroll through all the slices as expected.
Although that looked fine initially, when I saved the volume from there as a .nrrd, as I saw recommended here to preserve the 3D volume information, and opened the new .nrrd file, I completely lost the ability to see or scroll through the slices, and only had a single slice view. B I tried to import the data using the SlicerMorph ImageStacks extension like this instead, but ended up with a very strange looking volume that did not show up in the viewing planes:
The units feature in Slicer may not be working well in all cases, and since Slicer is natively in mm, such small numbers may not be well preserved. You might be better off just keeping track of the scale yourself so that the numbers for spacing are around 1, especially if you are going to do calculations or measurements of the data.
Looks like cool data - is it some kind of cell or egg? Share some 3D renderings if you get a chance.
Your imported volume has only one slice for some reason. That is being displayed, there is nothing else to display hence the other two views are just a single line.
Review your import procedure to make sure all frames from your multiframe tiff is imported.
Thanks for your reply! Once I can figure out how to get it imported correctly, Iāll try keeping the scaling ratio but just using larger units (maybe like 1.282 x 1.282 x 0.641 mm) and convert myself afterwards to see if that help!
Thanks, they are micro-CT scans of a small crustacean called an ostracod! Iām segmenting out and modeling their brain anatomy! They look like eggs because their bodies have an outer carapace around it, kinda like a clamshell.
Thank you so much for your reply! Yes, I see that, but I donāt understand why that is happening. When I add the file with āAdd Dataā normally, it seems to keep all the frames of the tiff. It is only after I add in the volume ā> imaging space information and save it as a .nrrd, or try to use the ImageStacks import that this happens. Am I entering the spacing information wrong? I also donāt know what the 4th dimension would be doing here, as the file is just a Z-stack of X-Y images.
This input size is weird, since normally it would be something like 883x1425x839, you have an extra 1 in the middle. Maybe you can tweak this some way in imagej to flatten it back to 3D. You say itās a āhyperstackā and Iām not sure what that is but maybe you can make it a regular āstackā instead. If this is a common kind of tiff file then if you can share an example maybe we can detect and fix it in ImageStacks.
Or, if you are handy in python Iām sure you can read the tiff into a numpy array and then make it a regular volume.
Also are you sure this is in micrometers (microns) as opposed to millimeter. 0.000641 would be like 0.641 nanometer. At that scale the length of your ostracod would be 0.5 microns, which doesnāt look right to me.
You are absolutely right I definitely meant to say 0.000641 mm or 0.641 microns! Thatās what I get for trying to operate on no sleep. Thanks for catching my dumb mistake here!
I definitely meant to say 0.000641 mm or 0.641 microns! Thatās what I get for trying to operate on no sleep. Thanks for catching my dumb mistake here!