We have confocal z-stacked images of mesenchymal stem cells from where we need to find the z value or the depth of the cell. We need the height values from the z-stacked cell images. How can we obtain that? Can anyone elaborate on the whole process?
If you used a computer driven microscope to capture the z-stack, the stage height should be stored in the metadata of the file. Where you can find this information will depend on what system/software you used.
John Hardy Lockhart Hi, thank you for your response. The z stack height is not provided in the software. The number of slices is shown over there like z=44 or z=94, like this, but that is not the height of the cell. I have captured the image under LEICA Stellaris.
You may have to go back to the microscope itself to easily find the z-coordinate of a given slice.
You can also try using the Bio-Formats Importer in ImageJ to open the file metadata using the "Display Metadata" option (see attached image, red box). This should provide the start and stop coordinates of your z-stack and the step size.
Thank you so much. I have not yet tried the metadata option. But have tried to use ImageJ's similar option. I will try this one.
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