Thread Subject:

overlaying fluorescent images

I would like to overlay microscope images with pseudo-
color and have the colors blend when necessary.

We have: three grayscale images from a microscope.
1. Background image that should stay in gray (living
cells, for those interested)
2. Fluorescence image taken with a specific wavelength
filter - a grayscale image that we know should only pass
say green. Shows stained items in image.
3. Same as above, but with red.

The fluorescent image is taken with a specific filter, and
I would like to pseudo color it and overlay on top of the
gray image. In addition, when the red and green coincide
we should get yellow...

How can I overlay those two and have the fluorescent part
nice and bright?
I have tried subimage and having two colormaps, but this
gives a pretty dark image and I am not sure if it merges
the overlaying colors.

Any help would be appreciated..

Daphne

On 22 Jan, 14:14, "Daphne " <daphnew_too_nos...@yahoo.com> wrote:
> I would like to overlay microscopeimageswith pseudo-
> color and have the colors blend when necessary.
>
> We have: three grayscaleimagesfrom a microscope.
> 1. Background image that should stay in gray (living
> cells, for those interested)
> 2. Fluorescence image taken with a specific wavelength
> filter - a grayscale image that we know should only pass
> say green. Shows stained items in image.
> 3. Same as above, but with red.
>
> Thefluorescentimage is taken with a specific filter, and
> I would like to pseudo color it and overlay on top of the
> gray image. In addition, when the red and green coincide
> we should get yellow...
>
> How can I overlay those two and have thefluorescentpart
> nice and bright?
> I have tried subimage and having two colormaps, but this
> gives a pretty dark image and I am not sure if it merges
> the overlaying colors.
>
> Any help would be appreciated..
>
> Daphne

Hi Daphne,

Unfortunately I can't help you with your specific problem as I only
just started working with fluorescent images that have been sent to me
and am not fully informed in who they were acquired. You may be able
to help me though. I am working towards a PhD (electrical engineering
profession) in which my current work involves analysing fluorescent
images of H35 cells to produce dynamic information of the gene
expression over time. In order to move in an appropriate direction
with my research I really need a good idea of what kind of image
processing is required in this area. Is it important to track cells
from image to image and specifically identify which ones are
expressing? Or maybe, is it simply enough to average the fluorescence
over the entire sample at each time period? Since you are working in
this field I would greatly appreciate if you could give me an idea of
the kind of problems you encounter with regards analysing the images
and what kind of information you really hope to achieve through this
analysis (no matter how far fetched the idea might seem at the
moment).

I'd appreciate any information you could give me.

Best Regards,
Alison

Alison - that really depends on what your research
question is.
Don't you have a PhD advisor to discuss this with?....

Daphne



alisonmcardle@gmail.com wrote in message <a8cc060d-d353-
41fa-a6ac-e95a6a0ddea1@v67g2000hse.googlegroups.com>...
> On 22 Jan, 14:14, "Daphne "
<daphnew_too_nos...@yahoo.com> wrote:
> > I would like to overlay microscopeimageswith pseudo-
> > color and have the colors blend when necessary.
> >
> > We have: three grayscaleimagesfrom a microscope.
> > 1. Background image that should stay in gray (living
> > cells, for those interested)
> > 2. Fluorescence image taken with a specific wavelength
> > filter - a grayscale image that we know should only
pass
> > say green. Shows stained items in image.
> > 3. Same as above, but with red.
> >
> > Thefluorescentimage is taken with a specific filter,
and
> > I would like to pseudo color it and overlay on top of
the
> > gray image. In addition, when the red and green
coincide
> > we should get yellow...
> >
> > How can I overlay those two and have thefluorescentpart
> > nice and bright?
> > I have tried subimage and having two colormaps, but
this
> > gives a pretty dark image and I am not sure if it
merges
> > the overlaying colors.
> >
> > Any help would be appreciated..
> >
> > Daphne
>
> Hi Daphne,
>
> Unfortunately I can't help you with your specific
problem as I only
> just started working with fluorescent images that have
been sent to me
> and am not fully informed in who they were acquired. You
may be able
> to help me though. I am working towards a PhD
(electrical engineering
> profession) in which my current work involves analysing
fluorescent
> images of H35 cells to produce dynamic information of
the gene
> expression over time. In order to move in an
appropriate direction
> with my research I really need a good idea of what kind
of image
> processing is required in this area. Is it important to
track cells
> from image to image and specifically identify which ones
are
> expressing? Or maybe, is it simply enough to average
the fluorescence
> over the entire sample at each time period? Since you
are working in
> this field I would greatly appreciate if you could give
me an idea of
> the kind of problems you encounter with regards
analysing the images
> and what kind of information you really hope to achieve
through this
> analysis (no matter how far fetched the idea might seem
at the
> moment).
>
> I'd appreciate any information you could give me.
>
> Best Regards,
> Alison