Category Archives: Calcium imaging

Preprint: Free head rotation while 2-photon imaging

We just posted the preprint for a method that allows 2-photon imaging while mice  freely rotate horizontally and  run around a real (or virtual) 2-D environment. The system allows attaching other instruments (ephys, opto, etc.) to the headpost. We think … Continue reading

Posted in Calcium imaging, Science | Comments Off on Preprint: Free head rotation while 2-photon imaging

GCaMP imaging in cortical layer 6

For my PhD work I made extensive use of 2-photon imaging of layer 6 cell bodies at depths of up to ~850μm using GCaMP. This is somewhat deeper than we (and others) have been able to image comfortably using other … Continue reading

Posted in Calcium imaging, Science | Leave a comment

Mirror alignment target for 2-photon microscopes

When aligning the laser path of a system in which mirrors are translated, like for instance for the x/y/z adjustments on a 2-photon microscope, the laser path needs to be kept in parallel with each of the translation axes. Also, … Continue reading

Posted in Calcium imaging | Comments Off on Mirror alignment target for 2-photon microscopes

Cheap dental drill

Common dental drills are useful/required to have in any systems lab. In addition to the usual applications, these can be used to cut holes in cover slides (diamond abrasive burrs), to cut small openings in drive implant bodies, smooth out dental cement, … Continue reading

Posted in Calcium imaging, Electrophysiology | Comments Off on Cheap dental drill

Simultaneous 2p imaging and visible-light optogenetics

We recently needed to verify how a large population of neurons reacts to weak optogenetic stimulation. We found that with a relatively straightforward setup, visible light optogenetic stimulation can be integrated into existing 2p rigs without resulting in problematic imaging … Continue reading

Posted in Calcium imaging, Open Ephys | Comments Off on Simultaneous 2p imaging and visible-light optogenetics

Maintaining local pixel cross-correlation in image registration

This post is about the effect of re-sampling in image registration methods on local pixel cross correlation for analyzing calcium imaging data. In awake 2p imaging, animal motion causes brain tissue motion and image motion. While z-motion that can not be recovered … Continue reading

Posted in Calcium imaging, Data analysis, Matlab | Comments Off on Maintaining local pixel cross-correlation in image registration