Scale Bar in DiameterJ Plugin


I am working on measuring collagen fiber thickness using both DiameterJ Segment and DiameterJ 1-018 plugins. I have successfully segmented the images but am unsure if I have entered in the correct scale bar for the DiameterJ 1-018 analysis. I believe my scale for the original image was 68 pixels/cm, which would convert to 680,000 pixels/micron. Does this value sound legitimate? It was taking my computer a long time to analyze the picture with this input so I had to stop the analysis. Thank you.

Hi @alemkuil

Let’s see - I’m not exactly sure the issue - but here are a few things to get the ball rolling…

  1. How exactly are you opening your images in ImageJ/Fiji? There are multiple ways to open images actually… but we recommend opening images via File > Import > Bio-Formats - that way your metadata is read in correctly. You can read up more on Bio-Formats here. Note: there were recent updates to Bio-Formats, so it’s always a good idea to consistently update Fiji, via the Updater, to stay as up-to-date as possible regarding all the plugins, etc. The newest version - 5.5.2 - was just released (see this forum post).
  2. What image format are you original datasets? What system are you using to acquire your images? You can use your imaging system - objective, camera, etc - to calculate your pixel size. For example, you can read up on that here.
  3. If you are having memory issues… you can make adjustments in your ImageJ installation… read up on this page regarding troubleshooting memory issues.

I hope this helps a bit!


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