Posting Images In The Forum

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In any case the provided image. Thank you for all your help. After all this time I have finally compiled a process that works consistently well. And evidently this thread you seem to still have some trouble. Please tell us if there are further problems. Just for completeness… the fill holes, as discussed is a binary image operation. However there is also a greyscale image hole filling procedure.

The morphology collection is available via the Morphology Fiji update site, and also here: The macro I use now:. You can use the image I posted at the beginning of this post. It comes out as odd shapes instead of consistently rounded edges for each bead.

As far as I remember you are interested in the object diameters and if computed appropriately they are not influenced by what you call odd shapes. This is another reason why I think there is some sort of problem with my image j. The only explanation I can think of is some sort of issue with an update. I have tried going back in recent upgrades and using different macros but nothing has really been solved.

I mainly was expected to use the protocol that others have been used in the past but it was developed by someone not as familiar with the system. I can run your macro but it still gives me a few odd shapes for objects that come up as circular using the macro that consistently work well.

The odd shapes are troublesome because I fear that they affect the posting images in the forum general area binary options edges diameter reading. Our results appear to be different as well. The general problem with these measurements is, how they are influenced by the previous processing. To answer posting images in the forum general area binary options edges question requires the knowledge of the latter posting images in the forum general area binary options edges.

Good day Taylor, this looks familiar to me. Here is a macro snippet: Herbie, Thank you for all your help. I have finally compiled a process that works consistently well. The macro I use now: TIF and doubtlessly there is a difference in favour of my approach. Herbie, You can use the image I posted at the beginning of this post. Please tell me if something is not as desired. This sounds quite obscure. Did you try my more recent macro and are the outputed diameters as expected?

Herbie, I have tried going back in recent upgrades and using different macros but nothing has really been solved. Herbie, I can run your macro but it still gives me a few odd shapes for objects that come up as circular using the macro that consistently work well. Ok fine Taylor and thanks! Why do odd shapes pose what kind of problem? What about the diameters, are they consitent with those gained by your approach?

Herbie, The odd shapes are troublesome because I fear that they affect the major diameter reading. To answer this question requires the knowledge of the latter … Thanks again and good luck Herbie.

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See attached Electron Microscope image a small section to start, keep it simple, images are much larger and more complicated. The image is a metal fracture surface.

Due to the stress placed on the material, horizontal cracks are formed, which need to be quantified once in binary form i have a macro down for it.

I took a quick 5 minute try at processing your image. I tried your suggestions, my results lead to excessive fragmentation. However, I do want to say that your are on the right track, which is FAR further than I would have ever gotten on my own. Sometimes I get an output, sometimes I get just an FFT which can be re-transformed, and sometimes I get nothing after a filter image.

This leads me to suspect a Gabor filter or variant may be where I need to go, but I am having troubles following the Gabor example macro and there is no plugin. Do you mean this Gabor filter example?? Or a different macro? I tried running the above Macro. Did you manage to get the Gabor filter working on your image?? If so, and results were not good, maybe tweaking below parameters will get you better results?

Or maybe you tried tweaking parameters and ran into problems? I had troubles following the example code logic to implement it. If it was a plugin already, I could try altering the parameters experimentally until it started to make sense in my head. By variant I meant stuff like Log Gabor filter - Wikipedia.

Using the Gabor filter script you can try to enhance the horizontal structures in your image. You just need a bit of patience to find the right parameters. Pasted image x KB. Here you are the exact script I used, which is a faster version than the one on the site since it uses FFT:. Inside the convolve the filter will be padded with 0 I think and there will be a discontinuity at the edge, and the properties of the filter are different.

The script I used is below it uses concepts from IJ2 and ops and is based on scripts presented here. Hello bnorthan and iarganda ,. One of the curses of my industries, being pulled off to fight another fire, has left me unable to try your suggested solutions right now. However, I appreciate the responses and wanted to take the time to thank you for looking into it.

I will try it as soon as I can manage it and get back to you. Just a reminder, the image I posted in general was a very small picture, the originals are about x pixels. I will have to play with the numbers to adjust for the more challenging areas. If you guys are curious, I can privately send you the full image. Need help in preprocessing to binary image Image Analysis. See attached Electron Microscope image a small section to start, keep it simple, images are much larger and more complicated Line Detection Test.

Reduce any shapes to a single line along the major axis Draw out the Feret Diameter? Hi Ajay I took a quick 5 minute try at processing your image. Hi bnorthan I tried your suggestions, my results lead to excessive fragmentation. Hello Ajay, Using the Gabor filter script you can try to enhance the horizontal structures in your image. Hello bnorthan and iarganda , One of the curses of my industries, being pulled off to fight another fire, has left me unable to try your suggested solutions right now.