Mask and measure

[AJBell]

Firstly if this has come up before, please accept my appologies, but I
could not find the answer on the list database.

For each FOV I have a phase and fluorescence image. What I want to be able
to do is to calculate the fluorescence per unit area of each object in the
FOV.

More precisely, I am trying to calculate the fluorescence per unit area
based upon the area obtained in the phase image (In effect, I have an
object that is sized in phase images, but is not all sizeable in
fluorescent images).

To do this, the obvious thing would be to create a mask of the phase image
and then use this to identify the ROI in the fluorescence images. However,
although I can make the mask, I can't seem to use it as the ROI for the
fluorescence images.

Is this even possible?

(Did that make sense to anyone?)

Thanks in advance

Andrew

[Pawel Znojek]

Hi
Try to split mask in Roi manager and then use individual selection for measuring fluorescence on second image
pawel

>-----Original Message-----
>From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of AJ
>Bell
>Sent: 20 April 2009 12:06
>To: [hidden email]
>Subject: Mask and measure
>
>Firstly if this has come up before, please accept my appologies, but I
>could not find the answer on the list database.
>
>For each FOV I have a phase and fluorescence image. What I want to be
>able
>to do is to calculate the fluorescence per unit area of each object in
>the
>FOV.
>
>More precisely, I am trying to calculate the fluorescence per unit area
>based upon the area obtained in the phase image (In effect, I have an
>object that is sized in phase images, but is not all sizeable in
>fluorescent images).
>
>To do this, the obvious thing would be to create a mask of the phase
>image
>and then use this to identify the ROI in the fluorescence images.
>However,
>although I can make the mask, I can't seem to use it as the ROI for the
>fluorescence images.
>
>Is this even possible?
>
>(Did that make sense to anyone?)
>
>Thanks in advance
>
>Andrew

[John Bradley]

Andrew,

I do something similar...

Once the phase image is thresholded, create selection (Edit>Selection>Create
Selection), then analyse particles with "add to ROI Manager ticked"
(Analyse>Analyse particles). This should give you ROIs. Click on your
fluorescence image and click Show All in ROI Manager.

hope that helps.

cheers, John

[AJBell]

Thanks, that works wonders! Incidently, is it possible to split ROI? By
that I mean when cells are touching they are picked up a one large object.
Is it possible in imageJ to seperate the ROI into the correct number of
cells? I know it is possible in other packages.

[Pawel Znojek]

Hi
Try to use Process/binary/watershed
cheers

>-----Original Message-----
>From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>Andrew James Bell
>Sent: 22 April 2009 10:14
>To: [hidden email]
>Subject: Re: Mask and measure
>
>Thanks, that works wonders! Incidently, is it possible to split ROI? By
>that I mean when cells are touching they are picked up a one large
>object.
>Is it possible in imageJ to seperate the ROI into the correct number of
>cells? I know it is possible in other packages.