![]() A 2 will appear in the lane when the rectangle is placed.ħ. Press 2 or go to Analyze>Gels>Select Next Lane to set the rectangle in place over the 2nd lane. Image-J will automatically align the rectangle on the same vertical axis as the 1st rectangle in the next step.Ħ. Center the rectangle over the lane left-to-right, but don’t worry about lining it up perfectly on the same vertical axis. You can also use the arrow keys to move the rectangle, though this is slower. Use your mouse to click and hold in the middle of the rectangle on the 1st lane and drag it over to the next lane. The 1st lane will now be highlighted and have a 1 in the middle of it.ĥ. After drawing the rectangle over your first lane, press the 1 key or go to Analyze>Gels>Select First Lane to set the rectangle in place. If you draw a rectangle that is short and wide, ImageJ will switch to assuming the lanes run horizontally (individual bands are vertical), leading to much confusion.Ĥ. ImageJ assumes that your lanes run vertically (so individual bands are horizontal), so your rectangle should be tall and narrow to enclose a single lane. Choose the Rectangular Selections tool from the ImageJ toolbar. The simplest method to convert to grayscale is to go to Image>Type>8-bit. The gel analysis routine requires the image to be a gray-scale image. Open the image file using File>Open in ImageJ.Ģ. This version of the tutorial was created using ImageJ 1.42q on a Windows 7 64-bit install.ġ. There should be very little difference between the results obtained from the various methods. You may prefer to use it instead of the methods I outline below. The method outlined here uses the Gel Analysis method outlined in the ImageJ documentation: Gel Analysis. See the references at the end of this tutorial for a discussion of the various ways that you can screw this step up. If you are scanning x-ray film on a flatbed scanner, make sure you use a scanner with the ability to scan transparencies (i.e. png or other image formats (.tif would be the preferred format to retain the maximum amount of information in the original image). This tutorial assumes that you have carried your gel or blot through the visualization step, so that you have a digital image of your gel in. ImageJ ( ) can be used to compare the density (aka intensity) of bands on an agar gel or western blot. Don’t use the alternate methods discussed on the old page, as they are subject to way too much user bias. ![]() The following information is an updated version of a method for using ImageJ to analyze western blots from a now-deprecated older page. ![]()
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