I’m a quite new Fiji user, and have met some problem while using Fiji.
I’m using Fiji to analyze the inflammation status of PBMC cell.
I have 3 individual color pictures. (Blue - Nuclei; Green - NF-ϰB; Red - Cytoplasm)
Basically, my idea is to use blue color picture to target the wanted cells (about 10 cells), then compare the area of green and red at the same location (wanted cells) to distinguish if it’s a inflammatory cell or not.
Procedure will be applied for 3 color pictures
- transfer pictures to 8 byte
- Adjust - threshold - default red
- Analyze - Analyze particle - Size around 4000 to 9000
Pictures will be like this -
I used “Wand (tracing tool)” to choose qualified (or target) cells on red and green color picture manually based on the target cells on blue color picture since it’s comparatively clear. Then used ROI to calculate the area of green and red color of the target cell, and use the Area (Green)/Area (Red) to determine the degree of inflammation.
However, since I have almost 1000 pictures to be analyzed, it takes forever to do it manually and I don’t have a strong coding background to write the command for automation. Thus, I came here for help.
- How to put a command to randomly choose 10 cells from blue picture
- How to apply ROI manager on the red and green color cells, based on the 10 cells chosen from the blue picture