Scanbox

New features for patterned photo-stimulation

By: darioringach February 1, 2025

N: Advanced Features, P: SLM, Segmentationgalvo-galvo, network commands, neuroscience, optogenetics, photostimulation, stChoME4 Comments

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…

A Narishige remote for Matlab

By: darioringach August 13, 2024

D: Motion Control and Knobbymanipulator, Matlab, motion control, motorized axis, narishige, system integration, virus injectionLeave a Comment

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…

Time-division beam multiplexing in Scanbox

By: darioringach October 7, 2022

B: Scanning Parameters, H: Laser Power and Pockels Cellfixed laser, multiplexing, scanbox, time-division, tunable laser, two photon imagingLeave a Comment

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…

Real-time, large-scale, processing in Scanbox

By: darioringach September 29, 2022September 29, 2022

Uncategorizeddeconvolution, memory mapped files, real time processing, scanbox, streamingLeave a Comment

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…

Easy z-stack with the ETL

By: darioringach August 18, 2022

J: Z-Scanning, K: Z-Stacks, Uncategorizedoptotune, scanbox, volumetric imagingLeave a Comment

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…

Error loading “ATSApi.dll”

By: darioringach August 5, 2021

UncategorizedATSApi.dll, error, MicrosoftLeave a Comment

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…

A one-line analysis pipeline

By: darioringach April 2, 2021April 13, 2021

Uncategorizedpipeline, Python, scanbox, suite2p, two-photon imaging3 Comments

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…

Real-time pose estimation with OpenCV in Scanbox

By: darioringach March 31, 2021

Uncategorizedbehavior, DeepLabCut Live, image processing, opencv, real time processing, scanboxLeave a Comment

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…

Real-time imaging and pose estimation

By: darioringach March 23, 2021March 23, 2021

Uncategorizedbehavior, DeepLabCut, DeepLabCut Live, Pose estimation, two-photon imaging6 Comments

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…

Event Panel

By: darioringach March 12, 2021March 12, 2021

Uncategorizedbehavior, event panel, imaging, integration, scanbox, ttl events, two photonLeave a Comment

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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