There is one hidden feature of Scanbox that has been around for some time, but I have not yet described. This feature allows for computer-assisted segmentation during an experiment. As you must already know, one way in which region of interests (ROIs) can be defined is manually. This process can be initiated by clicking on the Add button…
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Quick start guide to the Optotune and volumetric scanning
Scanbox uses an on-board current source to control the Optotune lens, so that changes in depth are synchronized to the beginning of each microscope frame. Once the lens is installed, the easiest way to verify its function is to start imaging a sample and move the slider in the Optotune panel to change the plane of…
Read MoreVisualizing Scanbox stacks with Vaa3D
Some scanbox functions allow you to export *.sbx files to *.tif files that can be then visualized using other software like Vaa3d or ImageJ. For example, after collecting a z-stack you can use sbxtifstack() to generate a tif file that can be read directly using Vaa3d. If your stack has the hypothetical file name abc_010_nnn.sbx…
Read MoreFast volumetric scanning with an electrically tunable lens
We have implemented volumetric scanning in Scanbox by means of Optotune‘s electrically tunable lens, which allows for fast changes in focal plane without moving parts. Some salient features of this particular implementation are: Laser power and focus can can co-vary, allowing the brightness of the images to remain approximately constant while performing volumetric imaging. This is achieved by…
Read MoreBidirectional scanning in Scanbox
We have implemented bidirectional scanning to Scanbox. To switch between bidirectional and unidirectional scanning all you have to do is hit the toggle button within the “Scanner” panel. The default setting is “U”, standing for unidirectional scanning; hitting the button will switch it to “B”, indicating bidirectional scanning. You can only switch between the two modes while the…
Read MoreAn active treadmill to control locomotion
As documented in several publications, active locomotion can strongly modulate cortical activity. I explained earlier how Scanbox uses a quadrature encoder to be able to control, in real time, an external stimulus that depends on the state of locomotion. In this way, we can design experiments in which stimuli are delivered during periods of locomotion or rest. However, if either locomotion…
Read MoreSimultaneous 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…
Read MoreBetter positioning with a wireless 3D mouse
The latest Scanbox release switches its positioning mechanism to rely on the 3dconnection wireless SpaceMouse. A single controller provides a more intuitive, responsive and smoother control of microscope position. It is more intuitive because the panning controls align with the axes of the microscope, and a twist motion of the knob allows you to rotate the…
Read MoreScanbox closes the loop with a quadrature encoder
If you have downloaded the latest version of Scanbox you may have noticed there is a new “Quadrature Encoder” panel and wondered what is does. In addition to ball tracking, you now have the option of tracking the 1D movement of a circular platform. The position of the platform is monitored by an optical quadrature encoder…
Read MoreNew features in latest Scanbox firmware
To take advantage of the new features in the latest release of the Yeti firmware you should start by getting rid of the half-wave plate control of the laser power. To do so start by removing the motor and half-wave plate from the optical path feeding the laser beam directly into the Pockels cell as…
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