Scanbox now allows interleaved scanning using tunable/fixed laser sources. If you are using such a laser (eg, Coherent Discovery TPC) the sliders in the Laser panel are configured to control the power of the tunable (left slider) and fixed (right slider) sources. Either before or during scanning one can choose to alternate stimulation with the…
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Real-time, large-scale, processing in Scanbox
We have expanded the real-time processing capabilities in Scanbox to deal with large number of neurons, while offering real-time image stabilization, raw fluoresence signal extraction, non-linear deconvolution and display of the results — all at video rates. Scanbox “Segment” button in the real-time panel can now be clicked after collecting ~2min data to automatically register…
Read MoreEasy z-stack with the ETL
New features in the volumetric scanning panel allows users to quickly populate the ETL table to perform measurements at equally spaced points. While scanning, simply move the ETL to the top of the volume you want to image and click the “Top” button to copy the location. Do the same for the bottom limit. Once…
Read MoreError loading “ATSApi.dll”
If when you start Scanbox, you get an error after the step “Setting up digitizer” that reads “There was an error loading the library ‘ATSApi.dll’. The specified module could not be found” proceed as follows: Go here and download the x64 version of the Microsoft C++ redistributable. Install it. Reboot your machine. Restart Matlab/Scanbox This…
Read MoreA 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…
Read MoreReal-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…
Read MoreReal-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…
Read MoreEvent 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…
Read MoreSuite2p 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…
Read MoreRolling 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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