ROI EXTRACTION MODULE (CELL-PICKER) Panel

Overview

The ROI EXTRACTION MODULE (CELL-PICKER) panel is used for extracting/generating ROIs to be used by the Photostimulation module. This module can be launched from the Stimulus Group Editor window:

After the ROIs have been generated within this module, the user can import them back into the Photostimulation window with the following option:

Main Toolbar

	Dropdown menu containing the options for extracting rois from an image.
	Turns off any active extraction algorithm and allows the user to manually select individual rois
	Dilates all selected rois.
	Erodes all selected rois.
	Removes all selected rois.
	Opens a settings window for filtering the image and setting algorithmic parameters.

No cell selection	No selection algorithm is currently active.
Disk cell	Uses an algorithm to detect disk-shaped cells. Uses the parameters set in the Settings window described in the next subsection.
Annular cell	Uses an algorithm to detect annular-shaped cells. Uses the parameters set in the Settings window described in the next subsection.
Manual mode	Adjusts alpha blending level between reference image and video stream
User defined	Uses a function

Sample User-Defined Function

function [xRoi yRoi] = roiUserDefFcn(rawImgData, filteredImgData)
	sizeImg = size(rawImgData);
	figure; imagesc(rawImgData);
	figure; imagesc(filteredImgData);
	disp('Drawing a roi in the top-left quadrant of the image');
	xRoi(1) = sizeImg(2)/4;
	yRoi(1) = sizeImg(1)/4;
	disp('Drawing a roi in the center of the image');
	xRoi(2) = sizeImg(2)/2;
	yRoi(2) = sizeImg(1)/2;
end

Settings Window

Pixel Range	An array setting the range of pixels that will be used in the internal representation of the image. Both the raw and filtered image are available in to the user.
Cell Radius Range	Sets the range of expected cell bodies in pixels. This is used by the procedures described above.
Divide by gauss-conv	Standard deviation of the a Gaussian to use to normalize the image. This is done by dividing the image by the convolution of the image with this Gaussian.
Colormap	Three-dimensional array defining the RGB colormap to use for the image.

ScanImage 2019 : Cell Picker Controls

Overview

Main Toolbar

Extraction Methods Dropdown-Menu

Settings Window

Attachments: