Re: Help needed with method of background substraction

Posted by khanas on Oct 31, 2014; 3:11pm
URL: http://imagej.273.s1.nabble.com/Help-needed-with-method-of-background-substraction-tp5010244p5010266.html

Dear Kees, 

Thanks for your reply!

I tried that option last night but with no success unfortunately. I just gave it another go in case I was being daft but no luck. 

I think the problem is that the image is at 16bit, and as that is the case ImageJ won't apply any changes in the LUTs - would you happen to know a way around this?

Thanks again for taking the time to write to me. 

Best

Abs

On Fri, Oct 31, 2014 at 11:23 AM, Straatman, Kees (Dr.) [via ImageJ] <[hidden email]> wrote:

Dear Abs,

Try if when you select under Analyze > Set Measurements the option 'Limit to threshold' your measurements are as expected.

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
University of Leicester
http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif

ImageJ workhops 15 and 16 December

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of khanas
Sent: 30 October 2014 15:32
To: [hidden email]
Subject: Help needed with method of background substraction

Hi all,

Have come across an image processing issue this morning and would really appreciate your help! Forgive my ignorance please I am quite new to microscopy/imageJ!

Essentially to quantify nanoparticle uptake into cells we take images with a whole cell fluorescent stain and a reflectance channel - the nanoparticles turn up in the reflectance channel and we use the staining to draw around a cell and analyse it for mean intensity.

To remove background reflectance other people in my lab have first split the channels of the image, and then using the max and min controls in B&C changed the min value until any background has been removed. After this they have selected the area in question (using the aforementioned stain), and then Measured mean intensity.

Unfortunately for some reason, potentially due to an update, it now doesn't measure between the values we set. it only ever gives mean intensity of the unedited/adulterated image and I have verified this by measuring the same area a few times with different Max and Min settings.

If I save the file as another format this can work but such a compression would be a problem from a quantification point of view!

A colleague just showed me this forum and I will have a look through to see if there are any existing solutions but any and all help would be very much appreciated!

Many thanks
Abs

Any help would be very much appreciated!

Thanks



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