#Imagej calibrate how to#

Notice that the images are not spatially calibrated, and their scale is reported in the top info bar in pixels, not real spatial units. Open the stage micrometer image, and the uncalibrated test image. Image of a stopped spinning disk confocal scanner head We want to measure the distance between the spots and the area of the spots. The same magnification was used to take the image on the right, a stopped spinning disk confocal scan head. Here’s an example: The stage micrometer image on the left shows 100 micrometers.

This assumes, of course, that both images are at the same magnification. The process of spatial calibration involves calibrating a single image against known values, then applying that calibration to your uncalibrated image. If that is so, then you need to spatially calibrate the image before you can measure distances and areas in it! If the image is NOT spatially calibrated already then the dimension will be labelled “pixels”. You can see that in the info bar at the top of the image, as there will be micro meters or some other spatial unit next to the numbers. If your image data was in a format that contained spatial calibration meta data, and Fiji (maybe using bio-formats) was able to read it, then your image might already be spatially calibrated. Suppose you wish to gather measurements from an image using real spatial units (µm, miles, etc), rather than just in “pixels”.

#Imagej calibrate how to#

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