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. …

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Reading 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…

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Memory-mapped data-sharing for real-time processing

To 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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