Processing is a versatile graphics language based on Java. Among other things, it provides a simple interface to process images using GLSL shaders. Here, I provide a simple example of a Processing sketch accessing the memory mapped data stream generated by Scanbox. This particular example simply posterizes the image using pre-defined shaders in Processing. Of…
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Using Suite2p with Scanbox
Marius Pachitariu and Carsen Stringer released a Python version of their Suite2p pipeline for two-photon imaging. So I decided to take this tool for a test drive with data collected from Scanbox. At the moment, Suite2p takes tiff and hdf5 files, so we first decided to write a function to convert *.sbx to *.h5 files. …
Read MoreSupport for Phenosys Speedbelt Linear Treadmill
Scanbox now provides a direct interface to Phenosys’ speedbelt. Once the speedbelt is connected via the USB to the computer it will show up as a COM port on the Device Manager. To acquire input from the treadmill, simply define the speedbelt_com configuration variable specifying the corresponding COM port. Within the Scanbox “Treadmill and Encoder”…
Read MoreProcessing Volumetric Data
After collecting volumetric data with the Optotune you can now process your data as follows. First, use sbxsplit() to generate separate data files for each “slice” of the optotune. For example, if I have a data file gn7_008_001.sbx collected some data with an optotune waveform having a period of 5 the command will generate a…
Read MoreNew alignment and segmentation tools
Improved alignment and segmentation tools have now been released in the latest version of Scanbox, while retaining much of the functionality of the last version. sbxaligntool. The new alignment tool, shown below, adds batch processing of files, including the processing of eye and ball motion if those data are present. A region-of-interest (ROI) can optionally be…
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Spikefinder: the Vanilla algorithm
Over the last few months, the Spikefinder challenge has provided a playing ground for colleagues to offer ideas about how to estimate the spiking of individual neurons based on the measured activity of fluorescent calcium indicators. The challenge was for people to come up with strategies that beat the performance of state-of-the-art algorithms, STM & oopsi. A good number of algorithms were able…
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 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…
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