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Hello,
I'm looking after a suitable way to eliminate scan lines on afm images without disturbing to much the image. I'm imaging alive bacteria into a porous membrane in liquid and when I display the height image, we can see some "scan lines" on the 3D image. Is there anyone knowing a way to eliminate these scan lines with an offline operation?
Regards
Guillaume
Hi Guillaume,
Both WSxM and Gwyddion have specific routines to do this. I am not aware if there is one in nano-scope software. Be aware, that you are altering the data (usually by averaging lines above and below) when you use these..for publication, the lines might be better than having averaged data....and they can skew your analysis as well.
Pete.
Nanoscope Analysis has three functions that can help with this issue (and they all alter your data set, so be careful):
1. Flatten can set adjacent scan lines to match in value or slope. Thresholding and exclusion boxes can help identify areas of good data.
2. Erase allows users to select lines or boxes to be replaced by the average of data above and below the selected region
3. Clean Image automatically removes streaks and spikes based on their size.
The online help for Nanoscope Analysis has more information. Instructions on how to download Nanoscope Analysis (for free) can be found here: Nanoscope Analysis v120r1sr3.pdf
Hope that Helps!
--Bede
Thanks Bede and Pete,
I'm aware about these manipulations could alter the data but it's for an illustration and not for an analysis. I'm already using Gwyddion and it works well for this kind of correction but I was looking after a similar solution in Nanoscope Analysis (before to post on the forum, I tried the solutions purposed by Bede by results aren't enought satisfying). Thanks for your help
Which function in Gwyddion are you using? We plan to make Nanoscope Analysis better over time...
match line correction
median line correction
step line correction
Bede,
I second to the idea to add similar function to any of the nanoscope software. We use it in WSxM. It is called "Flatten using paths". It allows one removing ugly parallel zones/changes of high of the image (mostly due to the laser jumps) without introducing artifacts which make it virtually impossible to derive real step height information.
Igor
_____________________________________
Igor Sokolov, Ph.D.
Professor,
Department of Physics,
Department of Chemistry and Biomolecular Science,
Director of Nanoengineering and Biotechnology Laboratories Center (NABLAB),
NY Center for Advanced Material Processing (CAMP) ,
Clarkson University,
Potsdam, NY 13699
Phone: 315-268-2375
Fax: 315-268-6610
http://www.clarkson.edu/~isokolov
http://www.clarkson.edu/~nablab
Thanks for your input. I'll add it to the list!