Pyscanbox

By: darioringach
Uncategorized, , , , , Leave a Comment on Pyscanbox

Santiago Jaramillo, one of our colleagues at the University of Oregon, has written pyscanbox, a public, lightweight Python/Qt interface for Neurolabware microscopes. The interface is designed to replicate in large part the Scanbox GUI, offering users who prefer a Python interface rather than Matlab. For a full list of which features are supported by his…

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New features for patterned photo-stimulation

By: darioringach
N: Advanced Features, P: SLM, Segmentation, , , , , 4 Comments on New features for patterned photo-stimulation

Here is a description of some recent features added to facilitated patterned photo-stimulation experiments. The first step, of course, is the definition of ROIs (or masks) to stimulate. After collecting some data from one field of view, you can either use the “Segment” button to have Suite2p detect the cells or manually draw them by…

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A Narishige remote for Matlab

By: darioringach
D: Motion Control and Knobby, , , , , , Leave a Comment on A Narishige remote for Matlab

I like the robustness and mechanics of Narishige products, but the electronics of the motorized controllers need to be updated to allow for remote control. I recently got this motorized axis, along with the compact controller. Unfortunately, the system has no way to be controlled via serial commands or any other way, which prevented us…

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Time-division beam multiplexing in Scanbox

By: darioringach
B: Scanning Parameters, H: Laser Power and Pockels Cell, , , , , Leave a Comment on Time-division beam multiplexing in Scanbox

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

By: darioringach
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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…

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Easy z-stack with the ETL

By: darioringach
J: Z-Scanning, K: Z-Stacks, Uncategorized, , Leave a Comment on Easy 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…

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Error loading “ATSApi.dll”

By: darioringach
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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…

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A one-line analysis pipeline

By: darioringach
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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

By: darioringach
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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

By: darioringach
Uncategorized, , , , 6 Comments on 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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