Sbxsegmenttool is a simple GUI that replicates the same mechanism used in Scanbox’s online segmentation to assist in the segmentation of cells and/or processes in data that has already been collected. Sbxsegmenttool expects the images to have already been rigidly aligned. After loading an *.align file, the mean mean aligned image will be shown momentarily and then replaced by a…
Read MoreA Scanbox user requested to add the ability to display a histogram of image values in real-time. Here, I use a the general mechanism of memory mapped files in Scanbox to show how easy is to add such “plug-ins” to provide additional functionality to the system. The Matlab code necessary to add real-time histograms in Scanbox is…
Read MoreScanbox is almost ready for in-vivo, two photon stimulation using spatial light modulators! In our first set of experiments we are are testing the system in SOM cells co-expressing C1V1 and GCaMP6. Prior to each experiment, we perform a calibration to ensure alignment of the SLM and imaging paths (takes ~3 min). Cells for stimulation are selected in the same fashion as we define ROIs for…
Read MoreWe 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 MoreSome 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 MoreIf 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 MoreScanbox 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 MoreMany 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…
Read MoreIf 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 MoreTo enhance the real-time processing capabilities of Scanbox we now provide a general mechanism to share frames being collected with another application running concurrently on the same computer via a memory mapped file. This general and flexible mechanism allows any user to extend the real-time processing of Scanbox beyond what is already offered. As an…
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