I’m a phd student and usually used imagej for other simple things and not for the quantification of the signal.
I have like 11 couple of chromosomes already processed…and I have to quantify the intensity of a BAC signal in red (the chromosomes are coloured in blu by DAPI). I tried to perform the measure but I’m not sure I do correctly.
Thanks for the attention.
No worries. Let’s see if we can all get you sorted… to start can you post the original image files you are working with? That way we have a better idea of your datasets, etc. Also - what workflow have you tried yourself already?
Too - here are a few helpful links regarding Segmentation in ImageJ/Fiji:
- 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 of the wiki
- “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.
Hi, here the image. The signals are FISH signals. I’m trying to quantify the intensity to find out if there are differences in it between homologous chromosomes. I’m using an image where the background was already removed, so I drew a line to obtain a plot profile of every single signals, and sametime I drew a rectangular area to obtain te value of integrated intensity. I dont know if this way is right or makes any sense.
Thanks for your help.