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Has anyone have an ideao if there is a way to remove the lines like the attached picture ? These are so called 'scatter' lines on a T.E.M. slide, made by a microtome.

enter image description here

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"scatter lines" is terribly confusing.... by "lines" do you mean the vertical pattern? Or by "scatter" do you mean the splotches? –  Scott Dec 5 '13 at 10:55
    
@Scott The vertical pattern is the scatter. It's a scientific term which is indeed rather ambiguous. It's caused, iirc, by light reflected back from the sample. –  Bakabaka Dec 5 '13 at 11:29
    
are they analogous with newton rings? –  horatio Dec 5 '13 at 16:26
    
@horatio: could very well be. I haven't used TEM in some 12 years, so my knowlegde's a bit rusty. –  Bakabaka Dec 6 '13 at 9:58

4 Answers 4

I did a quick textual search for information pertaining to TEM image post processing and the general method is to use Fourier transformation. There are several free Fast Fourier Transforms (FFT) plugins available for photoshop.

You would convert the image to RGB, run FFT on it which breaks the image into parts and uses the rgb channels to store them. Edit the Red channel (see inset, from top to bottom: after (zoomed); before (zoomed); before (unzoomed)) using the clone tool to clone data very close to the part you want to alter.

Run IFFT ("invert fft") filter on it, see inset. The amount of alteration depends on your skill and dedication to the task.

enter image description here enter image description here

A resource with great test samples showing how the patterns look under optimized conditions: http://www.qsimaging.com/ccd_noise_interpret_ffts.html

Note that for GD purposes, FFT is a great tool for descreening halftones and e.g. photo restoration

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I am impressed by the really great result. –  Takkat Dec 5 '13 at 17:34

There are probably several ways to do this, I just tried the one that came to mind first. It involves using paths which match up to each individual vertical line, then stroking them with the brush tool at an appropriate brush size/hardness onto the layer mask of a brightness adjustment layer. It didn't come out perfectly, but it could if one were to spend some time hunting down every last bit of vertical line. Whether this method would suit your purpose depends on the quantity of images you need to do this to, and how much time you have.

This animation shows the results with each added step of targeting specific lines for removal (I did 3 steps).

enter image description here

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In this case removing artifacts may lead to at least some improvements as we may use the somewhat regular striped pattern of darker an lighter areas scattered with noise the image has.

Rather than removing noise I added noise to the lighter areas to reduce the french blind banding artifact. We can do so by defining a brush, or by defining a regular fill pattern to aid us here.

  1. Select an area with fairly regular artifact bands to use as a fill pattern:

    enter image description here

  2. Use a bucket fill tool to fill the whole image with this pattern. Choose a darken mode to only apply the fill to areas lighter than the fill pattern.

  3. Flip the fill pattern horizontally and repeat the darken bucket fill.

    enter image description here

  4. We may need to choose another area pattern to repeat step 2.

  5. Reduce brightness and increase contrast until the result is satisfactory

    enter image description here

We can see that the banding artifacts could only be reduced but not entirely be emoved. This mainly comes from random irregularites in the original. We therefore need to play with different areas, or different sizes of the fill pattern we select. To entirely remove all banding artifacts there will however be no way other than go back to a very time consuming manual approach.

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+1 This was the first basic technique I thought of as well. –  horatio Dec 5 '13 at 17:22
    
@horatio: yeah but it turned out to be far more irregular than I was hoping. ;) –  Takkat Dec 5 '13 at 17:32

Only way I can think to do it is manually.

  1. Brightness and Contrast to eliminate most of the noise. Image > Adjustments > Brightness & Contrast...
  2. Bump Brightness up to about +100 and Contrast up to +100
  3. Go to Image > Adjustments > Levels...
  4. Select the white eye dropper in the popup window and select a gray pixel in the remaining lines to saturate the image with more white. enter image description here
  5. Grab the brush tool B and paint the remaining bits white as needed.

Result

enter image description here

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