Improvements in alignment and segmentation tools

Two GUIs to align (sbxaligntool) and segment (sbxsegmenttool) two-photon imaging data from Scanbox were recently updated.

Sbxaligntool allows users to perform alignment using rigid translation or a non-rigid deformation of the image stack. The tool now uses all the cores available in your computer along with the GPU.  Rigid alignment can take place at near 50 fps for 512 x 796 pixel images collected at 15.5 fps.  In other words, rigid alignment runs at more that 3 times the speed of data collection.


Non-rigid alignment is a bit slower. Still, running at 22 fps the system aligns images 40% faster than during acquisition.  In my system configuration the bottleneck of rigid alignment is in the disk system.   The bottleneck of nonrigid alignment is on the computation side, which could therefore be sped up by additional cores.


The segmentation tool also got a few improvements.  A pull-down menu provides the ability to zoom/pan within the image during segmentation.  The GUI now includes two different methods for segmentation–  region growing as described earlier, and a new SVD+kmeans automatic segmentation method.  You can switch between the two in a single segmentation session.  The Nhood variable determines the size of the local neighborhood used to perform the SVD+kmeans clustering.  At the end of the segmentation, after clicking Save and Extract, the extracted signals will be shown on the bottom of the window providing some qualitative assessment of the quality of the recording.


We will continue to improve these tools as we get user feedback.  So please, send bugs/suggestions our way. We are already working on extracting neuropil data and some basic post-processing (de-trending and deconvolution).