creating blobs from dim cells for quantification

Posted by vanessajune77 on Dec 12, 2013; 6:45pm
URL: http://imagej.273.s1.nabble.com/creating-blobs-from-dim-cells-for-quantification-tp5005890.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). 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 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 sample images.

Thank you again.

Vanessa

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