ScanImage 2019 : Cell Picker Controls




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.

Extraction Methods Dropdown-Menu

No cell selection

No selection algorithm is currently active.
Disk cellUses an algorithm to detect disk-shaped cells. Uses the parameters set in the Settings window described in the next subsection.
Annular cellUses an algorithm to detect annular-shaped cells. Uses the parameters set in the Settings window described in the next subsection.
Manual modeAdjusts alpha blending level between reference image and video stream
User definedUses 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;

Settings Window


Pixel RangeAn 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 RangeSets the range of expected cell bodies in pixels. This is used by the procedures described above.
Divide by gauss-convStandard 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.
ColormapThree-dimensional array defining the RGB colormap to use for the image.