I have downloaded diameter j but I don’t know how to use


I want to get the analysis results like this (see Annex). This is a SEM image of nanofiber. The author analyzed the average diameter of the 200 fibers in the picture, the maximum and minimum diameters, can you tell me how to do it? Thank you very much!

Dear @11118,

have you looked at the following resources?

If so, what are your specific questions?

Best,
Stefan

1 Like

dear @1118,
I have same question like you ,have you found the way to solve this trouble? I have been still in dilemma. COULD YOU TELL ME THE METHOD?

dear stelfrich,
I have read all you mentioned,and I download the software,I still cannot solve the trouble.THE trouble is same to this Error Message when using DiameterJ, you will undersand, I would be really appreacite you if you can help me.

If you have the same technical issue as the creator of the topic that you are referring to, then please post in this particular topic. Forking the discussion by posting in all the topics will not get you an answer faster and, speaking from my experience, is counterproductive.

2 Likes

you must use the older version of Fiji using Java 6, not the current Java-8 version:

  • Download the final Java-6 version of Fiji labeled “2017 May 30” from [here](https://imagej.net/Fiji/Downloads#Java_6).
  • Unpack it somewhere beneath your home folder.
  • Download diameterJ zip file> copy the zip file in new folder and extract it > open all the extracted folders (diameterj, skeleton analysis and orientationj ) and copy them into that installation’s plugins folder.
  • Launch Fiji and run *Plugins › 3D Viewer
  • Restart Fiji.
    open Fiji > open your image > set scale bar >Image > Type > 8-bit > save as 8-bit image in new folder
    open the saved 8-bit image in Fiji >plugin > DiameterJ Segment (NOT DiameterJ 1-018) > enter basic image information and select No in cropping location, select traditional too> select the folder of saved 8-bit image (not other folder) and wait till ‘‘command finished’’ appears in Fiji menu
    get out of Fiji> open the folder of saved image > open segmented image > check which image is best
    go to Fiji > plugin > DiameterJ 1-018 > select Yes for question: do you want diameterj convert … and enter scale bar information (you can find it in set scale) and select Okay> select the segmented image folder (not other folder) > wait till Fiji processes all segmented images > now you can get out of Fiji and go to the folder of 8-bit image > segmented image folder > in every folder you can see a few results that each of them is due to one of segmented image in segmented image folder

Q: When I run DiameterJ an error occurs that says “Unrecognized Command: “Skeleton Intersections”” or “Unrecognized Command: “OrientationJ”” or “Unrecognized Command: “Analyze Skeleton (2D/3D)”” or “Unrecognized Command: “Statistical Region Merging””

  • A: During installation one or more of the plugins that is needed for DiameterJ was missed. Please go back to the zip file that you downloaded for DiameterJ and copy all files into the plugins folder of ImageJ/Fij

you can watch this video too :https://www.youtube.com/watch?v=2M0j3ADP4bs