ImageJ questions & answers

ImageJ 1.41is a free Java image processing program
Question by Guest
May 24, 2016

I am a new user to ImageJ software. We use the software in conjunction with a Transilluminator for imaging of DNA gels in our laboratory. When we start up ImageJ and turn on the Transilluminator darkroom (table top model) and the UV lights on inside the darkroom, all we see is a white screen. I have played with the parameters, brightness/contrast, etc, and I don't know exactly what to do to possibly pinpoint what could be the problem? Is it some adjustment of the image parameters or is it likely the camera? Thanks.

Answer by Sean Hill

There is a vast documentation PDF guide available for downloading. You will have to get that PDF in order to find what's wrong with the software. I've searched the web and other websites, but nothing related was found. I recommend checking the PDF file because this is a way to overcome this issue you're having.

Question by Thingumy
June 25, 2015

I have a problem with calibrating images in ImageJ. I know the average intensities (i.e intensity over the whole sample) of my samples from different measurements, and I want to calibrate my images so that the pixel intensities (Gray Values) corresponds to the known intensity. I tried to calibrate images with Analyze > Calibrate by setting the measured mean pixel intensities on the left column and corresponding known average intensities on right (from two different samples). This gives negative minimum values, and obviously this is not what I want. Is there any ways to calibrate the image from known average intensity?

Answer by Robert Polubinski

There is a big user guide that teaches you how to configure and use the application. You can access it using the link below. You can use the information on the page for additional intensity configuration. There are also examples of how the configuration options will affect the results.

User guide:

Additionally, use the help from the websites listed through Google Search:

Question by Renee 1
October 21, 2012

I'm a beginner with ImageJ, so sorry if this is a basic question. I have many images of cells of which I would like to calculate the average total fluorescence. However, each time I take a measurement of the cell, it sets the max and min pixel values according to that particular image. So an image with clearly higher fluorescence values may have a lower average total fluorescence if only a couple of the cells have the fluorescence, whereas an image with all cells having barely any fluorescence will have a higher average fluorescence value. Could someone please let me know how would I be able to calculate the average fluorescence of the image according to a certain base point?

Answer by Sean Hill

There is already a document which contains a tutorial related to the ImageJ application. This tutorial refers to the intensity and how can you calculate it for a given image. As far as I can see, the intensity/fluorescence is calculated for each image individually. There is no base point to use as a standard calculation. Each operation needs to be done individually. Access Google then click the first link that downloads a DOC file.

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