I want to know if there ia a script/plugin for analyzing periodicities in amyloid fibrils in a batch mode. Analysing periodicities in individual images is a tedious task and I was wondering if there exists a script to process multiple images.
A 512x512 short image, starting at 0xa000...
How do you mean 'periodicity'? The width of the fibrils?
Only automated analysis program I know. Periodicity is the spacing between the very faint repeating features along the length of the fiber
http://www.sciencedirect.com/science/article/pii/S0003269711006646
Lambert, periodicity is the pitch of the amyloid fibril in a simple understanding
OK, I see the periodicity. Do you need an average value for all fibers in the image? If so, I can give it a try, but what is that value for this image, expressed in number of pixel-sizes?
Yes average value would be sufficient. since we have a many images, we would get an average with error. The image is 512 by 512 pixels and its a 10um by 10um image. so 0.0195 um/pixel.. Literature reports something around 88nm as periodicity values.
OK, I wrote a little program, and get a periodicity of 3.686 pixels. That would be too low. Visual inspection learns that the spread between fibers is high; there are strands that show a periodicity close to two pixels...
The image-file is three time the size of 512x512 short. Are there two more frames?
The method takes about 1 second, needs some fine-tuning, but could be publishable. Before I disclose the method, you need to agree that I will be pricipal co-author if you publish it. I wanted to pm you about this, but RG's mail-system seems to be down.
Lambert, i sent you a message. please check. To answer your question, the three images in the file are Phase,Ampliude and Height..We will use only the height images for periodicity analysis.
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