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…

Read More

Non-rigid image alignment in twenty lines of Matlab

We have previously discussed rigid and non-rigid image alignment algorithms for calcium imaging data. If you have the image processing toolbox, a particularly compact solution for non-rigid image registration can be written in ~20 lines of code or so.  The code below returns a displacement field for each frame in the image sequence (output variable ‘disp’) that needs…

Read More

Calibrating the Optotune

If you have been using the Optotune, you must have noticed that the values displayed within the optotune panel for the setting of the slider and the parameters of the z-scanning waveform are unit-less and not very useful. The latest update to Scanbox allows you to calibrate the Optotune and have all the units within the Optotune panel in micrometers.…

Read More

Scanbox Yeti (beta) has arrived!

Scanbox Yeti  is here! Why Yeti?  I don’t really know… but it sounds nice.  Future versions will take the names of other mythical creatures as well.  We should credit Josh Trachtenberg for this intellectual contribution to the project. We have been using Scanbox Yeti in the Lab for about a month without major problems and we…

Read More