I am new to imageJ and need help counting the number of neurons in this image.
I know I should find the threshold and do the “analyze particles”; but when I try doing it, it doesn’t accurately count the number of particles. Could you tell me the method so I can do it on my own next time thank you.
Welcome to the Forum and ImageJ in general.
So looking at your image - you can see that your sample varies across the background… you have a brighter background on the left side which diminishes as you move towards the right side. That is why a simple threshold won’t really work across the entire image.
You’ll have to do some pre-processing to deal with that background variation. Take a look at these older forum posts - you might find helpful:
Here are some other helpful links that you can use to get you started in Segmenting those cells (though know that things won’t be ‘perfect’ because of this background issue - just clean it up as much as you can):
- 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 - 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.
- MorphoLibJ plugin - another great tool for segmentation that comes with Fiji, providing more options/techniques… comes with Morphological Segmentation tool