Cell counter imagej fiji3/16/2024 We considered this magnification the most suitable to assess a reasonably large area without missing out cell morphology details. Acquisition: The macro was designed for images acquired with a 20x/0.8 air objective.Results are saved as an Excel (.xls) file. Threshold Sensitivity: Select the threshold protocol for cell counting.Ī processed image is generated and saved in a new directory. Channels: Choose the cells of interest in either the green, red, or combined channels.Threshold Sensitivity: Choose between a standard and high sensitivity threshold, in case you need to detect cells with low intensity values.Retina Area Selection: Choose between automated ONL & INL segmentation or manual freehand selection.If “Mostly not rounded“ is selected, mostly not circular cells will be counted (Circularity 0.0-0.5). If “Mostly rounded“ is selected, mostly circular cells will be counted (Circularity 0.5-1.0). Cell Roundness: If “All” is selected, all thresholded cells will be counted (Circularity 0-1).Minimum and Maximum Cell Area: Input the previously measured and selected cutoff values.The rescaled image will be saved as a copy. Image Rescaling Options: If the image is larger that 1300 pixels width, it will be rescaled to speed up the processing.Native Spatial Scale: Input the current image scale in pixels/microns.Image Native Resolution: Displays the imported image resolution.Microscope Magnification: Displays the working 20x objective magnification. Settings Dialog: Input the spatial scale obtained from the image metadata or microscope.Īfter importing a TIFF image and executing the counter, the following settings should be selected:
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