Re: Live histograms and overlays

[Nagesh Adluru]

nadluru <http://forum.imagej.net/users/nadluru>
September 22

Dear ImageJ community,

I posted this request on the new forum that Curtis Rueden mentioned but am
posting it also here in the hopes I can get help quicker.

Could you kindly help me with the following tasks

*1) Live histogram of "Z axis profile":* I have a hyperstack of images and
I would like to see "live histograms" of the Z-axis profiles. I can plot
the profiles but would like to see their histograms and preferably live.
The standard histogram command in the Analyze menu does this for line
profiles but not for the Z-axis profiles.

*2) Overlays of images with different LUTs and thresholds and transparency:* I
have statistical maps and underlying brain images. I would like to
threshold the statistical maps and use some colorful LUTs and overlay them
on the brain images (which themselves are in grayscale) so that the zero
values in the statistical maps are transparent. Once overlaid I am hoping I
can use "magic montage" to generate various presentations from it. I have
the magic montage macro working but the getting the right overlays has been
really challenging.

Thanks so much!
Nagesh

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

[ctrueden]

Hi Nagesh,

> I posted this request on the new forum that Curtis Rueden mentioned
> but am posting it also here in the hopes I can get help quicker.

Note that the forum post is here:
http://forum.imagej.net/t/live-histograms-and-overlays/37

And it already has multiple replies.

Regards,
Curtis

On Tue, Sep 22, 2015 at 7:05 AM, Nagesh Adluru <[hidden email]>
wrote:

> nadluru <http://forum.imagej.net/users/nadluru>
> September 22
>
> Dear ImageJ community,
>
> I posted this request on the new forum that Curtis Rueden mentioned but am
> posting it also here in the hopes I can get help quicker.
>
> Could you kindly help me with the following tasks
>
> *1) Live histogram of "Z axis profile":* I have a hyperstack of images and
> I would like to see "live histograms" of the Z-axis profiles. I can plot
> the profiles but would like to see their histograms and preferably live.
> The standard histogram command in the Analyze menu does this for line
> profiles but not for the Z-axis profiles.
>
> *2) Overlays of images with different LUTs and thresholds and
> transparency:* I
> have statistical maps and underlying brain images. I would like to
> threshold the statistical maps and use some colorful LUTs and overlay them
> on the brain images (which themselves are in grayscale) so that the zero
> values in the statistical maps are transparent. Once overlaid I am hoping I
> can use "magic montage" to generate various presentations from it. I have
> the magic montage macro working but the getting the right overlays has been
> really challenging.
>
> Thanks so much!
> Nagesh
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Nagesh Adluru]

Hi Curtis,

Thanks for the update. I checked out the replies and have some followup
questions. I replied on the forum itself.

Thanks again for your help!
Nagesh

On Tue, Sep 22, 2015 at 11:09 AM, Curtis Rueden <[hidden email]> wrote:

> Hi Nagesh,
>
> > I posted this request on the new forum that Curtis Rueden mentioned
> > but am posting it also here in the hopes I can get help quicker.
>
> Note that the forum post is here:
> http://forum.imagej.net/t/live-histograms-and-overlays/37
>
> And it already has multiple replies.
>
> Regards,
> Curtis
>
> On Tue, Sep 22, 2015 at 7:05 AM, Nagesh Adluru <[hidden email]>
> wrote:
>
> > nadluru <http://forum.imagej.net/users/nadluru>
> > September 22
> >
> > Dear ImageJ community,
> >
> > I posted this request on the new forum that Curtis Rueden mentioned but
> am
> > posting it also here in the hopes I can get help quicker.
> >
> > Could you kindly help me with the following tasks
> >
> > *1) Live histogram of "Z axis profile":* I have a hyperstack of images
> and
> > I would like to see "live histograms" of the Z-axis profiles. I can plot
> > the profiles but would like to see their histograms and preferably live.
> > The standard histogram command in the Analyze menu does this for line
> > profiles but not for the Z-axis profiles.
> >
> > *2) Overlays of images with different LUTs and thresholds and
> > transparency:* I
> > have statistical maps and underlying brain images. I would like to
> > threshold the statistical maps and use some colorful LUTs and overlay
> them
> > on the brain images (which themselves are in grayscale) so that the zero
> > values in the statistical maps are transparent. Once overlaid I am
> hoping I
> > can use "magic montage" to generate various presentations from it. I have
> > the magic montage macro working but the getting the right overlays has
> been
> > really challenging.
> >
> > Thanks so much!
> > Nagesh
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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