Analyze-Measure for multiple ROIs

[Sho Fujisawa]

I may be losing my mind, but I thought we used to be able to...

1) Create multiple ROIs (usually with Analyze Particles)
2) Use Analyze-->Measure (instead of RoiManager-->Measure) in order to get CUMULATIVE data on all ROIs. I don't need data from individual ROIs.

I can't do this any more, or I never could to begin with? What's a quick way to get cumulative data on all ROIs?


Sho Fujisawa
Sr. Digital Microscopist
Molecular Cytology Core Facility
Memorial Sloan-Kettering Cancer Center
417 E. 68th St.
Zuckerman Room 1834
New York NY 10065
[phone]
[phone]


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[Marcel]

You can still do this. Do you mean by cummulative data to the summary statistics?

However, in the Analyze particles dialog select the option "Add to manager".

After the measurements select the ROI's you want to measure (or select none to measure all).

Press the action "Measure" in the ROI manager dialog and then in the Results table invoke the action "Results->Summarize".

[Marcel]

To do this without the ROI manager just select in the Analyze Particles dialog:

"Display Results", "Summarize"

[Sho Fujisawa]

The Resutls-->summarize function gives me means and deviations. I want sum.

I can write a for loop to sum all the individual data, but it seems such a simple thing that can't there be a button for it?


Sho Fujisawa
Sr. Digital Microscopist
Molecular Cytology Core Facility
Memorial Sloan-Kettering Cancer Center
417 E. 68th St.
Zuckerman Room 1834
New York NY 10065
[phone]
[phone]

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Bio7
Sent: Friday, May 13, 2016 9:42 AM
To: [hidden email]
Subject: Re: Analyze-Measure for multiple ROIs

You can still do this. Do you mean by cummulative data to the summary statistics?

However, in the Analyze particles dialog select the option "Add to manager".

After the measurements select the ROI's you want to measure (or select none to measure all).

Press the action "Measure" in the ROI manager dialog and then in the Results table invoke the action "Results->Summarize".



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[Michael Schmid]

Hi Sho,

you can combine the ROIs in the ROI Manager with More>>OR (Combine).
With 'Measure', the measurement will be on the union of all ROIs (or all
selected ROIs, if there is a selection in the list of ROIs).

Michael
________________________________________________________________
On 2016-05-13 15:40, Sho Fujisawa wrote:
> I may be losing my mind, but I thought we used to be able to...
>
> 1) Create multiple ROIs (usually with Analyze Particles)
> 2) Use Analyze-->Measure (instead of RoiManager-->Measure) in order to get CUMULATIVE data on all ROIs. I don't need data from individual ROIs.
>
> I can't do this any more, or I never could to begin with? What's a quick way to get cumulative data on all ROIs?
>
>
> Sho Fujisawa

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[Marcel]

Yes, it would be the simplest to write a short macro and install it as an action if you need it often.

Here I found I nice macro examples:

http://imagejdocu.tudor.lu/doku.php?id=macro:calculating_stats_from_a_results_table

http://rsb.info.nih.gov/ij/macros/CustomTabStatFromResults.txt

[gankaku]

Hi Sho,

You could actually take your binary image and run the function >Edit
>Selection >Create Selection.
Then you need to make sure that really your foreground is selected. If this
would not be the case you can invert the select using >Edit >Selection
>Make Inverse. Then you just need to run the normal Measure command and you
will get the cumulative data from the complete over all selection. The Mean
gives you then the over all average intensity and the integrated density is
the sum of all pixel intensities.

If I understood your question correctly this should give you the result you
are looking for.

Regards,
Jan
Am 13.05.2016 15:40 schrieb "Sho Fujisawa" <[hidden email]>:

> I may be losing my mind, but I thought we used to be able to...
>
> 1) Create multiple ROIs (usually with Analyze Particles)
> 2) Use Analyze-->Measure (instead of RoiManager-->Measure) in order to get
> CUMULATIVE data on all ROIs. I don't need data from individual ROIs.
>
> I can't do this any more, or I never could to begin with? What's a quick
> way to get cumulative data on all ROIs?
>
>
> Sho Fujisawa
> Sr. Digital Microscopist
> Molecular Cytology Core Facility
> Memorial Sloan-Kettering Cancer Center
> 417 E. 68th St.
> Zuckerman Room 1834
> New York NY 10065
> [phone]
> [phone]
>
>
> =====================================================================
>
>      Please note that this e-mail and any files transmitted from
>      Memorial Sloan Kettering Cancer Center may be privileged,
> confidential,
>      and protected from disclosure under applicable law. If the reader of
>      this message is not the intended recipient, or an employee or agent
>      responsible for delivering this message to the intended recipient,
>      you are hereby notified that any reading, dissemination, distribution,
>      copying, or other use of this communication or any of its attachments
>      is strictly prohibited.  If you have received this communication in
>      error, please notify the sender immediately by replying to this
> message
>      and deleting this message, any attachments, and all copies and backups
>      from your computer.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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[Sho Fujisawa]

Yes, it is. I will try it out. Thank you!

Sho Fujisawa
Sr. Digital Microscopist
Molecular Cytology Core Facility
Memorial Sloan-Kettering Cancer Center
417 E. 68th St.
Zuckerman Room 1834
New York NY 10065
[phone]
[phone]


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of BioVoxxel
Sent: Friday, May 13, 2016 12:53 PM
To: [hidden email]
Subject: Re: Analyze-Measure for multiple ROIs

Hi Sho,

You could actually take your binary image and run the function >Edit
>Selection >Create Selection.
Then you need to make sure that really your foreground is selected. If this would not be the case you can invert the select using >Edit >Selection
>Make Inverse. Then you just need to run the normal Measure command and
>you
will get the cumulative data from the complete over all selection. The Mean gives you then the over all average intensity and the integrated density is the sum of all pixel intensities.

If I understood your question correctly this should give you the result you are looking for.

Regards,
Jan
Am 13.05.2016 15:40 schrieb "Sho Fujisawa" <[hidden email]>:

> I may be losing my mind, but I thought we used to be able to...
>
> 1) Create multiple ROIs (usually with Analyze Particles)
> 2) Use Analyze-->Measure (instead of RoiManager-->Measure) in order to
> get CUMULATIVE data on all ROIs. I don't need data from individual ROIs.
>
> I can't do this any more, or I never could to begin with? What's a
> quick way to get cumulative data on all ROIs?
>
>
> Sho Fujisawa
> Sr. Digital Microscopist
> Molecular Cytology Core Facility
> Memorial Sloan-Kettering Cancer Center
> 417 E. 68th St.
> Zuckerman Room 1834
> New York NY 10065
> [phone]
> [phone]
>
>
> =====================================================================
>
>      Please note that this e-mail and any files transmitted from
>      Memorial Sloan Kettering Cancer Center may be privileged,
> confidential,
>      and protected from disclosure under applicable law. If the reader of
>      this message is not the intended recipient, or an employee or agent
>      responsible for delivering this message to the intended recipient,
>      you are hereby notified that any reading, dissemination, distribution,
>      copying, or other use of this communication or any of its attachments
>      is strictly prohibited.  If you have received this communication in
>      error, please notify the sender immediately by replying to this
> message
>      and deleting this message, any attachments, and all copies and backups
>      from your computer.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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     and protected from disclosure under applicable law. If the reader of
     this message is not the intended recipient, or an employee or agent
     responsible for delivering this message to the intended recipient,
     you are hereby notified that any reading, dissemination, distribution,
     copying, or other use of this communication or any of its attachments
     is strictly prohibited.  If you have received this communication in
     error, please notify the sender immediately by replying to this message
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