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…
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Fixing a jittery, linear actuator
Do you hear a high-pitched noise when the port camera mirror is in one of the opened and/or closed positions? If so, it is possible the linear actuator is jittering a bit around its position. One way to solve this issue is to this install the Firgelli LAC configuration utility under yeti/firgelli. Follow the instructions…
Read MoreKnobby improvements
We have added a couple of new features to Knobby based on user feedback that some may find useful. These features are presented in different screen pages. You can switch between the three available pages by touching one of the 3 gray disks on the bottom left of the screen. The first screen is the…
Read MoreUpdating the trinamic firmware
Some updates to Scanbox/Knobby require the update of the firmware in the Trinamic TMCM-6110 card inside the motor controller. To update the firmware do the following: Run the program yeti/drivers/TMCL.exe Select Setup->Options from the menu. In the connection tab, select the COM port that corresponds to the card (it is typically labeled “Stepper”), and Click Ok.…
Read MoreKnobby updates
The last release of Scanbox provides a mechanism to update the firmware in Knobby and provides a few fixes to the existing version. We will be using this mechanism to deploy future improvements. The present version fixes a bug that incorrectly moved the objective to its original position when the X, Y, or Z axes…
Read MoreMeasuring the field of view and validating the uniformity of spatial correction
If you followed the instructions on spatial calibration you should have a nice uniform field in Scanbox. One simple way to measure the resulting spatial resolution and spatial uniformity at each zoom setting is to mount a 40 line pairs per mm RONCHI calibration slide on top of a green aut0-fluorescent slide. By aligning the…
Read MoreAuto calibration of SLM and two-photon paths
You’ve already heard about out plan to add an SLM path to the NLW two-photon microscope. As we described earlier the first step is to provide a tool to align the SLM and 2P paths. This is now complete and it consists of four phases carried out automatically by a Matlab function: A port camera connected to…
Read MoreA simple lick-o-meter and liquid reward delivery system
Some behavioral experiments reward correct performance. A typical response is a lick of a spout and the reward is a fixed volume of water. One simple way to achieve this is by using an Arduino board along with the capacitive sensing library. The diagram below summarizes the parts used. Just connect a 1 Mohm resistor between pins…
Read MoreUpgrading to Windows 10
Scanbox performance is better in Windows 10. We recommend the upgrade in general and highly if you use bidirectional scanning frequently. To upgrade, follow these steps. Upgrade to Windows 10. Make a fresh install of the lastest nVidia driver for your board. Install the latest 3D connexion driver. Install the latest AlazarTech driver for the 9440…
Read MoreInstalling knobby
Many of you will be receiving Knobby in the mail soon. Installing it is easy. Just follow these steps: Connect knobby to a USB port Open the Device Manager and check which COM port # knobby was assigned to (it is the one displaying an Arduino Due board). Open Matlab, edit scanbox_config.m and set the…
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