Hi! I am new in ImageJ, so please be kind! I am trying to quantify black stained fibers on histology images like the one attached. Is that possible using the threshhold tool?
Welcome to ImageJ and the Forum!
So… perhaps you can clarify a bit more…
- What are the ‘black stained fibers’ you are trying to Segment?
- When you say “quantify” - what exactly do you want to measure? Area? Curvature? etc.
Too - if you are really just getting started with ImageJ/Fiji - here are some helpful links:
- ImageJ wiki - the best place to learn everything about ImageJ/Fiji!!
- “Introduction to Fiji” workshop and corresponding slides- worth the time to get a solid intro
- Principles page - collection of principles for the entire image analysis process, from acquisition to processing to analysis
- Segmentation page
- “Segmentation in Fiji” workshop and corresponding slides
- Trainable Weka Segmentation (TWS) plugin and it is scriptable via macro code - a great tool for segmentation that comes directly with Fiji. NOTE: Fiji is Just ImageJ - it is simply a distribution of ImageJ that comes with a bunch of plugins bundled - ready for you to use out-of-the-box. If you are just getting started, we recommend downloading/using Fiji.