Applying 3D ROI to a non-segmented / thresholded image?

Posted by Snider, Kaitlin on May 06, 2014; 2:16pm
URL: http://imagej.273.s1.nabble.com/Applying-3D-ROI-to-a-non-segmented-thresholded-image-tp5007603.html

Hi :)


I'm fairly new to ImageJ, but I've spent a lot of time learning how to use the various available plugins etc over the last several months.  I have confocal .lsm Z-stacks in three channels, one of which is a nuclear stain.  I've worked with the Trainable Weka Segmentation to automate segmentation of nuclei vs. background, and then used binary, watershed, and analyze particles to get ROIs for each nuclei in each slice.  With the 3D ROI manager (http://imagejdocu.tudor.lu/doku.php?id=tutorial:working:tutorial_for_3d_roi_manager) I can take the segmented image and get great 3D ROIs.  What I'd like to do from here is use those 3D ROIs to then measure intensity values in the other two channels - un-segmented and un-thresholded.  The 3D ROI manager specifies that images should be segmented before loading, and trying it with the raw .lsm file just freezes the program (same if I convert to a raw .tiff file).  I can save and re-load the ROIs in the 3D ROI manager, but trying to load the 3D ROIs in Fiji's standard ROI manager onto the raw .lsm file just gets me an error.  Any ideas?  Is there a button I'm missing, or another plug-in that would help transfer the 3D ROIs to the raw image?


Link to the raw .lsm image: https://drive.google.com/file/d/0Bw4MsPRmUoyISWU2aGNRalBRNjQ/edit?usp=sharing

Link to the segmented binary nuclei image: https://drive.google.com/file/d/0Bw4MsPRmUoyIUnFPWkNheXV4cVk/edit?usp=sharing

Link to the 3D Objects file for the segmented image: https://drive.google.com/file/d/0Bw4MsPRmUoyIVjFuS0VNNjA1NTg/edit?usp=sharing

?Thanks very much for your time :)


Kaitlin Snider

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