distance from vessels to hypoxic regions

[Caroline Bouzin]

Dear all,

I would like to measure the distance between vessels (labeled with CD31 - red fluorescence) and hypoxia regions (pimonidazole staining - green fluorescence) in tumor sections.

According to what I read in this specific field, here are the operations that I tried so far:

I first converted the image with vessels to a binary image, inverted it and applied a distance map.
The pimonidazole image was thresholded and converted to a binary image.
Then, I went to the image calculator and I admit that I am lost with the different operations (multiply, XOR,...) and I don't know which one is the more appropriate here.
Also, on images resulting form image calculator, I don't understand which kind of values are then displayed (distance from vessels? unit of these values?).

Thank you in advance for any suggestion, comment...
Caroline

[Christian Goosmann-2]

Hi Caroline,
I think you have the right ideas. Did you consider, instead of using
image calculator, to convert the pimonidazole image to objects by
'analyze particles' while redirecting them to roi manager and then
measuring each object (= roi = hypoxia region) in the distance map
image? You can choose the measurements by 'set measurements'. The min
intensity of an hypoxia object would be the pixel distance from the next
vessel. The values in the distance map vary with the image type. If you
choose 16-bit they can go as far as your image boundaries if it is
8-bit, it is 0-255 for the first 255 pixels and 255 for any greater
distance in pixels.
Hope this helps
Christian

---
Christian Goosmann
Mikroskopie
Max-Planck-Institut für Infektionsbiologie
Campus Charité Mitte
Charitéplatz 1
10117 Berlin
Tel.: [phone]

Caroline Bouzin wrote:

> Dear all,
>
> I would like to measure the distance between vessels (labeled with CD31 -
> red fluorescence) and hypoxia regions (pimonidazole staining - green
> fluorescence) in tumor sections.
>
> According to what I read in this specific field, here are the operations
> that I tried so far:
>
> I first converted the image with vessels to a binary image, inverted it and
> applied a distance map.
> The pimonidazole image was thresholded and converted to a binary image.
> Then, I went to the image calculator and I admit that I am lost with the
> different operations (multiply, XOR,...) and I don't know which one is the
> more appropriate here.
> Also, on images resulting form image calculator, I don't understand which
> kind of values are then displayed (distance from vessels? unit of these
> values?).
>
> Thank you in advance for any suggestion, comment...
> Caroline
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/distance-from-vessels-to-hypoxic-regions-tp5004659.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Michael Schmid]

Hi Caroline,

the distance map (EDM) has its values in pixels. If you set Process>Binary>Options to get a 32-bit (floating point) EDM, you can multiply it with the size of a pixel to get physical units such as mm.

With a 32-bit distance map, the easiest is working with selections (rois):
Create a roi for object of interest (hypoxia region) and find the minimum of the distance map for the roi ('Measure').  If you have several rois, you can use 'Analyze particles'  on the mask of the objects (hypoxia regions) and redirect the measurement to the distance map. Make sure you have 'min&max' checked in the 'Set Measurements'.


Michael
________________________________________________________________
On Sep 5, 2013, at 13:35, Caroline Bouzin wrote:

> Dear all,
>
> I would like to measure the distance between vessels (labeled with CD31 -
> red fluorescence) and hypoxia regions (pimonidazole staining - green
> fluorescence) in tumor sections.
>
> According to what I read in this specific field, here are the operations
> that I tried so far:
>
> I first converted the image with vessels to a binary image, inverted it and
> applied a distance map.
> The pimonidazole image was thresholded and converted to a binary image.
> Then, I went to the image calculator and I admit that I am lost with the
> different operations (multiply, XOR,...) and I don't know which one is the
> more appropriate here.
> Also, on images resulting form image calculator, I don't understand which
> kind of values are then displayed (distance from vessels? unit of these
> values?).
>
> Thank you in advance for any suggestion, comment...
> Caroline
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/distance-from-vessels-to-hypoxic-regions-tp5004659.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Caroline Bouzin]

Thanks a lot for your kind (and quick) help.
It's working!
Caroline