Volumetric analysis

Recently I’ve started using ImageJ for fluorescent signal detection in synapses (double or triple labeling proteins of interest with synaptic marker synapsin, collecting images, thresholding, masking, analyzing intensities/histograms).
ImageJ is very powerful program and so far I apply analysis to single optical slices.
Does anyone know how can I measure it volumetrically? Can I built volumetric reconstruction and apply analysis mentioned above to this entire 3D structure (using voxels or some other units)?

Hi Timur,

We successfully analysed synaptic elements and are currently working on spine detection. you can have a look to our publication : https://www.ncbi.nlm.nih.gov/pubmed/25001083 . Please feel free to contact me or the first author for details.

Thomas

Hi Thomas, This is great publication and procedure is generally outlined. However I had difficulties trying to learn segmentation (first step for building volumetric structure). Can you please let me know the way how can I build volumetric structure from the confocal stack using segmentation?

Hi Timur,

First to understand segmentation you may wqant to use simple but efficient tool like 3D Objects Counter :

http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:3d_object_counter:start

Try to find a manual threshold that can detect your object and then segment your objects. Then you can add this segmented image to the 3DManager for analysis :

http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_roi_manager:start

hope this helps

Thomas