I need to put images from a micrsoscope together to line them up to one set of pictures …. I would like the software to do this as it would be A LOT of work to do that manually ! I want the software to match overlapping cells, etc together so that the pictures fit to each other. Does anyone know how to do this with which SOftware ?
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I understand exactly what you are asking, as I had to do this very same thing from microscope (confocal scope in my case) images! I have yet to find a software that will automate the process, as the finding and aligning of the cells is a very subjective thing. You might be able to use a stitching program, but it will still require effort on your part to line up the images.
PS can do the job for you if you know that you need to move one picture, say 20 pixels up and 40 pixels left, for each of the images. You can make an action to do the job for you. There are others here that are more knowledgable than I on this issue. I’m sure they would be willing to help you set it up if you think that actions are the way to go.
I would do it by hand. Only you know which added image needs alignment, rotation or other manipulation. It’s best to work using one or two 23" cinema displays and open all of your images at once. select all for each image and paste into one new large canvas that you have created to become the final document. When you paste, the images will each go to their own new layer – so you can have full control over each new addition. Simply get started as it goes rather quickly once you get started. Save the Photoshop original canvas then flatten all the layers and save under a new name in the format you need.
Using a solid white background, I paste each image onto it’s own layer. You can then temporarily make the new layer around 40% or 30% transparent to line up the images. (rotate as required) Once a layer’s lined up, make the transparency 100% again, clean up any edges you need to and merge it down. To be safe, you can skip the merging and save all the lined up layers file as a psd file for a backup. Merge all the layers in one step when you are completed and save as a tif, eps, etc.
I have yet to use software that stitches images better than a human(some of them) can.
I’m not sure how your microscope images are obtained but when using scanned photos or images, they might not be correctly rotated. The auto-stitch will try to fit them together anyway producing a messy line.
It sounds to me as if they are using a Confocal Microscope to gather their images and then have to manually layer one image over another to get the "full picture". It’s a tedious job, that’s for sure! I just don’t see an automatic way of combining those images, since there are so many variables and subjective alignments that need to be done. I had to combine 6 sets of 110 images each (sort of like putting 6 loaves of bread together – each image was a slice of bread) to graphically recreate the full "specimen".
Mark and Ken are suggesting reasonable ways to do this tedious reconstruction.
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