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Creating one Histogramm out of multiple ROIs in a stack

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imagej_user1

Creating one Histogramm out of multiple ROIs in a stack

Hi everyone,

Could somebody help me with the following problem:
I Have a stack of images and in some slices, I create ROIs. (Not in all slices).
Now, I would like to determine the summarized Histogramm of all these ROIs.

When I select all ROIs and press "H" it only shows me the Histogramm of the ROI first selected.
I don't want to measure "all slices", I just want to measure the different ROis in some slices all at once.

When I select all ROIs I want and press the OR (Combine) command in the More >> menu, it creates a new ROI in one of the selected slices. But this is also not what I need. I have to consider that the ROIs come from different slices. and the intensity has to be measured at precisely the slice where the where constructed.

Hope you can understand me and I'm very much looking forward to hear from you,

Imagej_user1

Jan Eglinger

Re: Creating one Histogramm out of multiple ROIs in a stack

Hi,

someone (maybe you?) posted the same question on the ImageJ forum:

http://forum.imagej.net/t/creating-one-histogram-of-multiple-rois/667

In that discussion, I posted an example script that sums up the
histograms of all ROI selected in the ROI Manager.

Hth,
Jan

On 25.01.2016 12:32, imagej_user1 wrote:

> Hi everyone,
>
> Could somebody help me with the following problem:
> I Have a stack of images and in some slices, I create ROIs. (Not in all
> slices).
> Now, I would like to determine the summarized Histogramm of all these ROIs.
>
> When I select all ROIs and press "H" it only shows me the Histogramm of the
> ROI first selected.
> I don't want to measure "all slices", I just want to measure the different
> ROis in some slices all at once.
>
> When I select all ROIs I want and press the OR (Combine) command in the More
>>> menu, it creates a new ROI in one of the selected slices. But this is
> also not what I need. I have to consider that the ROIs come from different
> slices. and the intensity has to be measured at precisely the slice where
> the where constructed.
>
> Hope you can understand me and I'm very much looking forward to hear from
> you,
>
> Imagej_user1
>
>

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Herbie

Re: Creating one Histogramm out of multiple ROIs in a stack

In reply to this post by imagej_user1

Good day NoName,

evidently this is a cross-post from the ImageJ-Forum.

If I understand correctly, you wish a single histogram from several ROIs
each of which is in another slice of a stack.

Why not loop through the slices of your stack and get the histogram
values of every slice by using the macro-command "getHistogram(...)".
Then you can add up the various histograms and that's it. If you want to
visualize the final histogram values then there are example macros that
show you how to do that. Have a look at the example macro
"HistogramPlotter.txt".

HTH

Herbie

::::::::::::::::::::::::::::::::::::::::::
Am 25.01.16 um 12:32 schrieb imagej_user1:

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imagej_user1

Re: Creating one Histogramm out of multiple ROIs in a stack

In reply to this post by Jan Eglinger

Hi Jan,

thank you very much I'm trying out your proposal.

Thanks,
imagej_user

imagej_user1

Re: Creating one Histogramm out of multiple ROIs in a stack

In reply to this post by Herbie

Hey Herbie,

it is true that I could add up the single histogramms (I actually do it like this right now).
But I have a lot of data and it's not only one time that I have to summarize the histogramms.
So this is why I asked since I think there is for sure a more elegant and efficient way to do it.

Thank you for advising me the HistogramPlotter.

I continue the conversation on the link that Jan posted.
Right now, I'm not yet sure which platform is the better to post things, so sorry if there was double posting.

imagejuser

Herbie

Re: Creating one Histogramm out of multiple ROIs in a stack

You wrote:

"But I have a lot of data and it's not only one time that I have to
summarize the histograms."

Does this mean that a macro is too slow for the processing?

I really can't imagine that this is true.

Somehow puzzled

Herbie

::::::::::::::::::::::::::::::::::::::::::
Am 25.01.16 um 16:01 schrieb imagej_user1:

> Hey Herbie,
>
> it is true that I could add up the single histogramms (I actually do it like
> this right now).
> But I have a lot of data and it's not only one time that I have to summarize
> the histogramms.
> So this is why I asked since I think there is for sure a more elegant and
> efficient way to do it.
>
> Thank you for advising me the HistogramPlotter.
>
> I continue the conversation on the link that Jan posted.
> Right now, I'm not yet sure which platform is the better to post things, so
> sorry if there was double posting.
>
> imagejuser
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Creating-one-Histogramm-out-of-multiple-ROIs-in-a-stack-tp5015449p5015454.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_user1

Re: Creating one Histogramm out of multiple ROIs in a stack

Sorry Herbie,
I misread your suggestion.
I'm doing all this right now manually since I'm not yet familiar to macros etc. I read over the 'Macro' in your sentence.
But Jan also recommended me this Macro on his linked posting above.
I try to get it running, thank you