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In this section of the workshop we are going to cover adjusting images to make up for deficiencies in the acquisition systems or specific problems with acquiring the image. Now let's get something straight right now. It's the researcher's goal for each and every image that they collect to be a true representation of the sample. On top of that each image collected stands alone in how best to acquire that particular image. The imaging equipment has to be in proper working order, calibrated and set up to the best of your ability to acquire unbiased images that have the correct exposure. An example of this is setting up proper color illumination on a microscope. If you don't do that you've already hobbled your acquisition system and your images will be poor.
The use of image processing to adjust an image should be to compensate from limitations in the equipment or samples. Over the next few videos I will be using various pictures that have been either scanned in or images collected directly from a digital camera connected to a microscope. In many cases these show specific problems that we can now overcome using image processing software. But software cannot make up for poor scientific technique. Garbage in will be garbage out. Take the time to get the best image as possible because even when you manage to accomplish this, there will be other problems inherent that you will need to fix.
In general, you need to consider how any image processing will affect the legitimate use of an image. Second, you should always track and fully disclose any image processing accomplished on an image. Third, where possible use non-destructive methods, in other words, where you are not actually changing the pixels but you are just changing the way the pixels are presented to you. And lastly and most importantly for scientific use the corrections to be based on standards and controls and then apply the same changes directly to the experimental images.
It wouldn't be right to necessarily process this image in Photoshop. Anything you could do might change the density of the bands and alter your analysis. This is what you are stuck with and you need to realize when image processing should not be done. Accept it and move forward. Now let's go to our first challenge.
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