The latest Scanbox release brings a major performance improvement. The main bottleneck in the acquisition loop consists of a function that re-arranges the incoming pixel stream into the images that are displayed and stored in real-time. This function now makes use of OpenMP to distribute the work among different physical cores available in your machine…
Read MoreA montage display for real-time display of volumetric data
By default, Scanbox displays the incoming image stream on its main window. Thus, during volumetric scanning, one sees the incoming images as depth is changing over time. If one is imaging only a handful of optical planes, it is difficult to see what is really going on. A different way to visualize the data in…
Read MoreA rolling average plug-in for scanbox
Scanbox offers a memory-mapped interface mechanism to expose incoming data to other processes. This facilitates a wide rage of customization by users that may want to display their data in different ways or do some on-line processing not currently supported by Scanbox. We previously provided one example of how a real-time histogram of the data can…
Read MoreReading scanbox files in Python
One quick way to get your data into Python is by using the Matlab API for Python. First, install the MATLAB engine API for Python by following he instructions here. You will need to install as administrator. Then, from your Python code you can simply do, as an example: This will read 50 frames starting at index…
Read MoreImprovements in alignment and segmentation tools
Two GUIs to align (sbxaligntool) and segment (sbxsegmenttool) two-photon imaging data from Scanbox were recently updated. Sbxaligntool allows users to perform alignment using rigid translation or a non-rigid deformation of the image stack. The tool now uses all the cores available in your computer along with the GPU. Rigid alignment can take place at near…
Read MoreA plug-in for real-time histograms in Scanbox
A 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 does 2p-SLM stimulation! (And the mystery of the disappearing cell)
Scanbox 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 MoreNon-rigid image alignment in twenty lines of Matlab
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…
Read MoreFixing 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…
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