Scanbox

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…

Suite2p reads Scanbox binaries

By: darioringach March 12, 2021March 12, 2021

Uncategorizedpipeline, scanbox, suite2p, two-photon1 Comment

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…

Rolling average

By: darioringach February 12, 2021February 13, 2021

Uncategorizedrolling averageLeave a Comment

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…

Adjusting the illumination

By: darioringach December 3, 2020

Uncategorizedepifluorescence, illumination, intrinsic imagingLeave a Comment

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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