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How do I make the image from one channel a mask to use to measure images in another channel?

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Dan

How do I make the image from one channel a mask to use to measure images in another channel?

This post was updated on .

I am trying to convert my blue DAPI images in to masks to then measure deferences in intensity in the red channel (so I only take measurements of the red channel where it is co-localised with blue). I have tried creating duplicate images and making them in to mask images but, so far, can only use the masks to analyse the image it was created from, rather than images taken in another channel.

If anyone has any suggestions I would be very grateful.

Thanks,

Dan

Kenton Arkill

Re: How do I make the image from one channel a mask to use to measure images in another channel?

Hi
If they are not separate: image/colour/split channels to separate.

Create the mask as you do on the dapi, so it is (binary) black and white (make it the same bit depth as the interesting image), then multiply that mask onto the one would want using process/image calculator
nb when multiplying use 32bit option. (if you need it 8bit afterwards divide the whole thing by 255).

Regards
Kenton

On 15 Nov 2012, at 16:24, Dan wrote:

> I am trying to convert my blue DAPI images in to masks to then measure
> deferences in intensity in the red channel (so I only take measurements
> where the two channels are co-localised). I have tried creating duplicate
> images and making them in to mask images but, so far, can only use the masks
> to analyse the image it was created from, rather than images taken in
> another channel.
>
> If anyone has any suggestions I would be very grateful.
>
> Thanks,
>
> Dan
>
>
>
> --
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> Sent from the ImageJ mailing list archive at Nabble.com.
>
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Jacqueline Ross

Re: How do I make the image from one channel a mask to use to measure images in another channel?

Hi Dan,

You could also create regions of interest (ROI) from the DAPI image and put those into the ROI Manager. Then just load those onto your other image and use the Measure button from the ROI Manager.

I usually do it this way by counting the number of nuclei first using the particle analyzer, which creates an ROI for each nucleus and loads it into the ROI Manager for you. Then I click on the other image and show the ROIs there and then measure. The advantage is that you then get values for each individual nucleus, including those which have no labelling. Plus you get all the data in one results list. Make sure you select Display Label in the Set Measurements window so that you get the name of the image plus the ROI info.

Kind regards,

Jacqui
________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Kenton Arkill [[hidden email]]
Sent: 16 November 2012 05:56
To: [hidden email]
Subject: Re: How do I make the image from one channel a mask to use to measure images in another channel?

Hi
If they are not separate: image/colour/split channels to separate.

Create the mask as you do on the dapi, so it is (binary) black and white (make it the same bit depth as the interesting image), then multiply that mask onto the one would want using process/image calculator
nb when multiplying use 32bit option. (if you need it 8bit afterwards divide the whole thing by 255).

Regards
Kenton

On 15 Nov 2012, at 16:24, Dan wrote:

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