Thresholding cell blob

Posted by vanessajune77 on Nov 12, 2013; 5:43pm
URL: http://imagej.273.s1.nabble.com/Thresholding-cell-blob-tp5005540.html

Hello ImageJ Listserv,

Thank you in advance for your help. I am a new user and am using ImageJ to quantify colocalization. I am using Fiji and CoLoc_2 plugin, (I have the ROI manager plug-in as well) and am aware of the Bio-format plug-in for .lif files. I can check my images for direct information loss and choose multiple ROI's in manager.
I have cells that have bacteria colocalizing with the cell's lysosomes. So where I don't know:

1) threshold out the cell borders. determine ROI (each cell) using tools like Blob, threshold, analyze particles etc. This is important because bacteria within a certain distance of the cell will be used in study and those father away will not be analyzed for colocalization with lysosomes.

Once ROI is determined then I believe I will run analysis on each bacteria with in that distance from the cell (blob) to determine what percentage of bacteria are colocalizing.after I have the procedure down I would like to do this using the Bioformat plug in to use on Z-stacks.

Thanks for any input on this and how to threshold out my cells. I have attached a sample image. Thank you again.

Vanessa




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