Sorry, I m a scientist in aquaculture without any background in image processing. I m looking for a help to understand how can I calculate a distance between 16 landmark in rainbow trout Photo. I know that is easy if we have 2 or 10 Photo. But we released a trial and we took a 300 photos of deferents fish.
The question could we use imageJ to do this process? or existing plugins in Fiji to do it
We can help or suggest you better if you could share a sample image & tell exactly what you want to measure. In the meanwhile, hope these articles might help,
Thank you Lakshmi for these papers
I join a photo with all the landmarks, our idea is to
- Calculate the distance between all of them,
- Calculate fish surface
we realised a trial with different diets and we need to compare morphology traits,
Though I am not sure how to get the landmarks, to answer your first question ,
calculate distances is not available as a direct plugin, one may have to write a macro to compute it. This has be already done in the below thread. You can also try the same script in your case as well.
How to batch measure distances between points
To compute surface, you have to threshold & check in any of the measurements helps you.
These are the steps I followed to threshold. Screenshot here,
crop 2. Split the channels to separate RGB 3. Threshold the Red channel. 4. Convert to mask 5. fill holes 6. Analyse particles to compute the measurements
Hope this helps,
Thank you @lakshmi is so helpful