I have a Trichrome slide, I’ve used trainable weka segmentation to define different classifiers. My question is what to do after getting all classes done? I mean I get some stacks of image consisting seperated classes, But for example I want to measure the amount of blue connective tissue in the ROI, how to do that? Or amount of scar tissue.
Do you have any better suggestion to measure different aspects of this slide? for example a plugin or …
I’m really new to ImageJ.
I need sets of plugins to help me measure different aspects of a histolgy slide. can you list them for me? Of course letting me know what to do with weka after processing.
(Vascularization, Connective Tissue and …)
I Attach one sample image.
Welcome to the Forum!
Once you generate your probability maps, you can use them to auto-threshold, create a mask, and then analyze particles… to generate ROIs. You can then do whatever specific measurements you need using Set Measurements and Measure. For more on Segmentation, check out these links:
It may be that you need something a bit more ‘tailored’ - in that case you should look into Scripting. And trust me - even if you have no experience writing code - ImageJ is a great place to start! So again - here is a list of helpful links to get you started with that:
- Scripting overview page on the wiki (already linked above)
- A helpful workshop on Scripting with Fiji - the slides are here
- Introduction into Macro Programming page of the wiki
- Built-In Macro Functions list - a full list of macro functions you can easily search…
I hope this helps a bit! If you have more questions - just post again.
I’ll try them and will inform you in following days. Thanks.