Remove light/dark lines

[nikopol]

   

First of all, sorry if I post in the wrong section and if for some the answer seems obvious.

I did some research but did not find the solution to my problem.
I want to remove light and dark vertical and horizontal stripes that appear on my image. 
These lines appear because the image is composed of 200 thumbnails stitch together. The areas of overlap and the difference in brightness and contrast of each tiles make these light and dark lines appear.
If you have a step by step solution (I am a beginner) I am greatly interested.
Thanks in advance

[rich2005]

Are these microscope images?

How were the individual images stitched together? Can you give details of how that is done. Your jpeg image file name gives a small clue but more details will certainly help.

[nikopol]

(09-20-2018, 02:22 PM)rich2005 Wrote: Are these microscope images?

How were the individual images stitched together? Can you give details of how that is done. Your jpeg image file name gives a small clue but more details will certainly help.

:-) yes, these are transmission electron microscope images. The real image consists of 180 (4k x 4k) tiles. Images were acquired with ShotMeister and then stitched together with Fiji (=ImageJ, some parameters of the stitching sequence are in the file name as you noticed: fusion method=linear blending and fusion alpha set to 1). Neither average, nor max intensity, nor min intensity for the fusion method remove these lines.

[rich2005]

I think the real solution will be use some other application for stitching the images together. Nip2 is the tool for large mosaics but difficult to use, or you might get Hugin to work.

Using Gimp you might get a fix using the g'mic plugin http://www.gmic.eu One of the filters in the repair section local similarity mask

A screenshot using your small jpeg https://i.imgur.com/myDqvbf.jpg You will have to play with the settings, it will produce a new layer. Put that layer in multiply mode. https://i.imgur.com/ZBPseu3.jpg

Might/might-not work, I do not really know what it should look like

[nikopol]

It should look like a hepatitis cell with nucleus, golgi apparatus, mitochondria etc.... ;-) but without these stripes.

You talked about Hugin, I will give it a look, not sure it will successfully work (ICE from Microsoft failed) but I'll try it. Nip2....!!! Yes it seems difficult to use and I don't have enough time to get my hands so dirty....

g'mic plugin will certainly be my first try... even if I was hoping a quick and simple solution with isolating the dark areas and subtracting them from the original image (see image attached)

Anyway thanks for the potential avenues...