Bada boom! New system coming soon!

So why the long silence in the Scanbox blog?

We have been working hard on a the development of our new system. A modular, expandable system that will run the new line of Neurolabware microscopes (aka the Kraken microscope) and is backward compatible with our previous box.

Want a sneak peak?

Bada boom!



Here is a closeup of some of the LCD/power modules…



If you are interested in the new features of the Kraken microscope and the new modular system please get in touch with Neurolabware.

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).


Simultaneous control of an electrically tunable lens and a pockels cell

We are preparing Scanbox for fast, volumetric scanning, by providing simultaneous control of an electrically tunable lens (to focus on different planes) and a Pockels cell (to control laser power).

The Scanbox card has an integrated, 12-bit current source used to control the focus tunable lens. Similarly, an integrated DAC on the Scanbox card controls laser power via a Pockels cell. The mechanism implemented still allows for user-defined blanking of the margins.  Arbitrary tables can be uploaded from the Scanbox GUI to the card to allow for simultaneous changes in these variables that are precisely synchronized to the frames of the microscope.

Below is a demonstration showing a sinusoidal change in focusing along with matching changes in laser power.  Fast scanning with synchronized depth/power control is coming to Yeti soon!

[vimeo 119605807 w=500&h=280]