Currently I use “Reconstruct Synapse Web”, made available by the Harris lab at the University of Texas at Austin. Although I am very familiar with this software and do enjoy using it, it requires me to segment all of my TEM series manually. I am looking for a segmentation program that is at least somewhat automated in order to increase my efficiency in taking blocks of tissue to the reconstruction stage. I have heard that the Lichtman group at Harvard utilizes a program called ”Mojo” to do this but I have been unable to get the program to work for me from its link on their website. If any of you know a suitable program that you have used could you please let me know?
cheers
Ian
Out here , I write codes for segmenting the images (sem-automated ) using MATLAB
May be Photoshop
Dear Ian,
maybe this is interesting:
Article SynEM, automated synapse detection for connectomics
Regards,
Andreas
May be you can use ImageJ/Fiji for opening TEM series. For semi-automated segmentation including seed/region growing and 3D construction, you can also use Slicer (https://www.slicer.org/) or MITK (http://mitk.org/wiki/The_Medical_Imaging_Interaction_Toolkit_(MITK))
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