When imaging at low magnification in bidirectional mode cells can be small, with a diameter of ~6 pixels or so. In this and other situations the mechanism offer by the ncolbi variable to align even and odd lines may prove too coarse for optimal alignment. We added a new variable to the configuration file, named…
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Important enhancements in Scanbox 3.3 firmware
Good news! The latest Scanbox version in Github includes a few important improvements and fixes: The new firmware substantially decreases line jitter producing even shaper images. It removes the artifactual horizontal lines from the mean of bidirectional scanning acquisitions. It fixes a bug in the phase of the camera trigger signal. It checks for cases where no…
Read MoreLatest Scanbox Release brings cool performance improvements
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…
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Sbxsegmenttool: A simple GUI for off-line segmentation
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 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…
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