Getting Started:
Downloading and Using FIJI/ImageJ
I use this resource for almost everything I need to do with images in FIJI
<aside> 🔗 https://monashmicroimaging.github.io/gitbook-fiji-basics/
</aside>
Analyzing Brain Image Specifics:
Merge Images: "Image" > "Stacks" > "Z Project" > "Max Intensity"
Cell counter function : manually count and label cells by clicking on them individually, one at a time
Open Image First: "File" > "Open..." > Select Imag
"Plugins" > "Analyze" > "Cell Counter" > "Cell Counter"
"Initialize" and select type
Click on each cell to manually count
Results window shows counts
Cell Counter User Guide: https://imagej.net/Cell_Counter
Use Macros to automatically count
"Macros" > "Run" > Select file from download location
OR to save in Fiji: "Plugins" > "Install..." > Select file > save in plugins folder
Tip: Use the quick search in FIJI to find plugins and run them
Highlight a specific area on image then click "OK"
SGDAPI3 function: use on DAPI images, outline the area you are counting with line segments then press "OK," number found under "Count" on "Summary" page
Macro Oct 15 DAPI function: also DAPI images