A one-line analysis pipeline

With the ability to read Scanbox binaries in Suite2p I wrote a one-line processing pipe-line for Scanbox. If you are within a data directory with folders you want to process, all you have to is pass a list of the experiments to sbxsuite2p(): This example just contains a list of two experiments. Matlab will then…

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Real-time pose estimation with OpenCV in Scanbox

We previously describe how we can incorporate DeepLabCut models to run concurrently to Scanbox to provide real-time pose estimation while imaging. Of course, the mechanism for communicating with DeepLabCut is general enough to allow processing by other means. In some simple cases, just as detecting the center of the pupil doing two-photon imaging, simple image…

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Real-time imaging and pose estimation

I’ve made substantial progress to read real-time DeepLabCut Live date (see paper by Kane et al here) from Scanbox. As you can see in the example below, I got to the point where we can do two-photon imaging and pose estimation in real time. As you recall, the behavior cameras in Scanbox are triggered once…

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Event Panel

An updated event panel provides real-time information about TTL events and allows you to provide a name, which is then used to create a matching field in the file metadata. First, this allows for the user to detect if all required events are coming in as expected during the experiment (as opposed to finding out…

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Suite2p reads Scanbox binaries

Thanks to the work of João Couto, Suite2p now reads *.sbx files. I just processed some of our data and it works nicely. You can download Suite2p from here. Some of the metadata are currently missing, as they are stored in a Matlab’s object that is not easily read in Python, but I will be…

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Rolling average

We previously showed how a rolling average of the input stream can be computed with a Scanbox-plugin. As many users seem to be making use of this feature, we now include the rolling average as an integrated feature of Scanbox. This only applies to the Pizza Box version of Scanbox. The video below shows where…

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Adjusting the illumination

If you are using the port camera on the microscope to acquire intrinsic and/or epi-fluorescence imagery, it is helpful to have a tool to adjust the illumination to be even across the sample such that no regions are saturated. A new illumination checkbox is now available in the camera panel: When the camera is on,…

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Achieving high frame rates with subframe folding

Scanbox samples, transfers and processes one frame at a time. Frame processing involves correcting for non-uniform spatial sampling along the resonant axis, motion stabilization, real-time extraction of signals, displaying the images, streaming to disk, and so on. This overhead in frame processing can limit the maximum frame rate achievable if the computer cannot keep up…

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A Processing sketch plug-in

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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Optogenetics with the Tower

The optogenetics panel in the new Tower electronics (aka the Pizza Box) is nearly the same as its predecessor. The main difference is that synchronization and timing of stimulation is done internally and does not require any external electronics. The parameters at the bottom specify the width of the LED, GATE pulses and the number…

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