Welcome to Scanbox!

Welcome to Scanbox File Exchange.  This is a site where you can find regular updates to the scanbox software for two-photon imaging, report bugs, share data analysis tools and ideas for improvement.

As time goes by we will be posting tips and tricks on how to use the software, insights into the code (the Matlab software is open to the community), and documenting the various functions you can use to analyze the data.

Some of features already implemented in the release version of ScanBox:

  • Two analog and two digital channels sampled at laser frequency (80Mhz) and 16-bit depth.
  • Control of PMT gains.
  • Non-uniform spatial sampling correction in real time (raw data are streamed to disk).
  • Real time averaging and display of data.
  • Uniform power density over scan line by modulation of Pockels cell (an arbitrary waveform can be programmed).
  • Control X, Y, Z stage and tilt angle of objective.
  • Z-stack data collection
  • Movement in a rotated coordinate system that keeps the (x,y) plane normal to the objective.
  • Control of laser parameters (power, shutter, wavelength).
  • Two additional TTL signals timestamped with the frame and line number where they occurred.
  • Two GigE cameras synchronized to the microscope frame to acquire eye pupil/position and ball movement.
  • Additional GigE camera for intrinsic imaging through the same (or different) objective.
  • Additional digital I/O, I2C, SPI, current generator (for electrical tuned lens) expansion capability.
  • Remote control of the microscope over the network (change file names, start acquisition, stop acquisition, etc).
  • Matlab software for reading data, motion correction, segmentation, and signal extraction.

At the heart of the system is an AlazarTech 9440 digitizer and a custom-designed card based on the PSoC 5LP 32-bit ARM-based processor from Cypress that is in charge of generating the scan signals, generate trigger signals for the cameras, timestamp external TTL events, and more.  The card communicates with the host computer through a USB serial line.

That’s it for a quick introduction…  but, before leaving, here is one of the first movies we obtained with the microscope in Josh Trachtenberg’s Lab showing 1 min in the life of prefrontal cortex (please don’t ask me what I was doing there).  Enjoy —