Sbxsegmenttool: A simple GUI for off-line segmentation

Sbxsegmenttool is a simple GUI that replicates the same mechanism used in Scanbox’s online segmentation to assist in the segmentation of cells and/or processes in data that has already been collected. Sbxsegmenttool expects the images to have already been rigidly aligned.  After loading an *.align file, the mean mean aligned image will be shown momentarily and then replaced by a…

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Non-rigid image alignment in twenty lines of Matlab

We have previously discussed rigid and non-rigid image alignment algorithms for calcium imaging data. If you have the image processing toolbox, a particularly compact solution for non-rigid image registration can be written in ~20 lines of code or so.  The code below returns a displacement field for each frame in the image sequence (output variable ‘disp’) that needs…

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Online cell segmentation in Scanbox

There is one hidden feature of Scanbox that has been around for some time, but I have not yet described. This feature allows for computer-assisted segmentation during an experiment. As you must already know, one way in which region of interests (ROIs) can be defined is manually.  This process can be initiated by clicking on the Add button…

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Using auto-stabilization

Real-time auto-stabilization in Scanbox Yeti is achieved by tracking the displacement of 2D features in a number of small windows relative to a reference image.  We prefer tracking cells within a handful of small windows because slow gradients in the image can easily bias the resulting estimates for large regions. Here are some step-by-step instructions on how…

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Real-time, motion compensation in Scanbox

Our colleague Tobias Rose was recently asking about Scanbox’s ability to stabilize the motion of images and signals from regions-of-intrest (ROIs) in real-time.  The goal of such processing is to be able to do experiments in closed-loop, and do very quick analyses on the neuronal responses, such as computing tuning curves on the fly. Below is a…

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Sorting calcium imaging signals

Originally posted on xcorr: comp neuro:
Calcium imaging can record from several dozens of neurons at once. Analyzing this raw data is expensive, so one typically wants to define regions of interest corresponding to cell bodies and work with the average calcium signal within. Dario has a post on defining polygonal ROIs using the mean fluorescence…

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Real-time signal extraction, visualization and processing in scanbox 2.0

Here is a sneak preview of the new features to be released with Scanbox 2.0. Some of the salient additions include: Automatic stabilization: The system can automatically correct for rigid (x,y) translation in real time. Selection of regions of interest (ROIs): Allows for the selection of regions of interest that need to be tracked in real-time.  After their definition,…

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Reading raw data with sbxread()

Raw image data in scanbox is contained in *.sbx files.  To read these data you can use the sbxread() function. Here is the documentation from its help section– So, for example, the following lines of code will read images from 0 to 19 (20 total) and display the average of the first (green) PMT channel: And you may…

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Non-rigid deformation for calcium imaging frame alignment

Originally posted on xcorr: comp neuro:
It’s been a while since I last updated the blog – I graduated from McGill, went on a trip to Indonesia where I did a lot of diving (above), came back to Montreal for 16 hours to gather my coffee machine and about three shirts – all I need to survive, really – then moved…

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basic processing pipeline

Scanbox includes some basic processing functions that you can use to (a) align the images to compensate for (x,y) movement, (b) segment cells, (c) extract the signals corresponding to the segmented cells from the image sequences. Motion compensation (sbxalignx & sbxaligndir) The first step that is sometimes required is to compensate for motion in the…

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