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Home > Scale Bar Tools for Microscopes

Scale Bar Tools for Microscopes

Friday 15 May 2009, by Gilles Carpentier

  Table of contents  


  • Calibrate your objectives:

    The present method is a very simple way to calibrate your "microscope-camera couple" with enough precision for most of current applications. It requires to take the image of a micrometric grid for each used magnifications.
    The next figure shows such an image, taken with an objective from magnificance "6,3". The space between each bars corresponds to a known distance of 100 µm.
    To measure a pixel distance, select the straight line tool, and draw a line selection parallel to the scale axis.
    Select the "Analyse/Plot Profile" function. Place the cursor at the level of the first peak, and note the "x" value. Do the same for the last peak. The difference in the exemple, from 436 pixels corresponds to a known distance of 500 µm (0.872 pixel/µm).

    Another easier way is described in the ImageJ documentation, at this link. The precision of this method depends on the user appreciation of the maximum of intensity of the scale graduations, especially for high magnification.

    The result, 0.875 pixel/µm, is quite similar to the previous measurement method in that case.

  • Create a microscope profile:

    Using the results of the previous measurements, select "Microscope Profile Manager Menu -> Create a New Microscope Profile", choose a name, and fill the fields value for the objective N° 1, as shown in the next picture and validate the dialog box.

    The new profile is now visible in the "blue microscope" menu. Select the created profile.

    Open an image and click on the "Scale Bar" icon, choose the objective, the tool is ready to scale images.

    To add another objective, select "Microscope Profile Manager Menu -> Edit & Modify a Microscope Profile", and proceed in the same way.

logoij ImageJ ( is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.1 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux. The author, Wayne Rasband (, is at the Research Services Branch, National Institute of Mental Health, Bethesda, Maryland, USA.
Gilles Carpentier, Faculte des Sciences et Technologie,
Universite Paris Est Creteil Val-de-Marne, France.

Special thanks to Alessandra Albano for the English correction of these sites.
Computer Data Acquisition
for Biochemistry Practice Works
Image analysis tools in biology
and biochemistry using ImageJ