Re: simultaneously obtaining ROI and measurement data

[David Nauen]

Hello,

I've searched the forum archives and found related threads but did not find
the answer to my question -- I have an image containing multiple structures
of interest.  I measure each using the line tool followed by Ctrl-M. Then I
add each measurement line as an ROI, holding Shift as I click Add in the
ROI dialogue to keep the measurement line displayed.

With dozens of of structures to measure in every image it would be much
better if I could capture the ROI data (where is the line) at the same time
I capture the measurement data (how long is the line).

Is there a way to capture both types of data in one step?  What about
keeping successive measurement lines displayed?

Thank you
David

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[jchanson]

You can get the line location information by adding the bounding rectangle data to the measurement output (Under Analyze | Set Measurements...).  You should know everything about the line from the BX, BY, Width, Height, and Angle values.
It doesn't solve the problem of keeping the successive measurement lines displayed, though.

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of David Nauen
Sent: Monday, May 06, 2013 7:26 PM
To: [hidden email]
Subject: Re: simultaneously obtaining ROI and measurement data

Hello,

I've searched the forum archives and found related threads but did not find the answer to my question -- I have an image containing multiple structures of interest.  I measure each using the line tool followed by Ctrl-M. Then I add each measurement line as an ROI, holding Shift as I click Add in the ROI dialogue to keep the measurement line displayed.

With dozens of of structures to measure in every image it would be much better if I could capture the ROI data (where is the line) at the same time I capture the measurement data (how long is the line).

Is there a way to capture both types of data in one step?  What about keeping successive measurement lines displayed?

Thank you
David

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[Christine Labno-2]

Hello David,

If you use the ROI manager under Analyze --> Tools --> ROI manager, you can use the t key to add a line to the ROI manager in place of shift click, you can use the show all checkbox to keep ROIs displayed as you draw them, and you could even use the More --> MultiMeasure tool to measure all of your lines at once, after they are drawn.  

Does this help you?
Best,
Christine
--------------------------------------------
Christine Labno, Ph.D.
Asst. Technical Director
Light Microscopy Core
University of Chicago
Office of Shared Research Facilities
KCBD 1250 900 E. 57th St.
[phone] (phone)

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of David Nauen [[hidden email]]
Sent: Monday, May 06, 2013 6:26 PM
To: [hidden email]
Subject: Re: simultaneously obtaining ROI and measurement data

Hello,

I've searched the forum archives and found related threads but did not find
the answer to my question -- I have an image containing multiple structures
of interest.  I measure each using the line tool followed by Ctrl-M. Then I
add each measurement line as an ROI, holding Shift as I click Add in the
ROI dialogue to keep the measurement line displayed.

With dozens of of structures to measure in every image it would be much
better if I could capture the ROI data (where is the line) at the same time
I capture the measurement data (how long is the line).

Is there a way to capture both types of data in one step?  What about
keeping successive measurement lines displayed?

Thank you
David

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[David Nauen]

Thank you for the suggestion, but there are so many structures I need to keep the measurements displayed so I don't duplicate.

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[David Nauen]

Thank you, that is great, these steps definitely help.  

Now I need to modify my analysis algorithm to interepret the large table of measurement data I generate with multi measure, but it looks straightforward to extract the lengths.  I might be able to use the other values ('mean','min', and 'max') if I understood what they refer to.

I also need to figure out how to export the values from ROI manager;  I'm using linux and in ROI Manager under More, the Save dialog seems only to offer a zip file option, which generates a directory where every x,y ROI value pair becomes the name of a separate file.  Can't seem to cut/paste from ROI Manager window either ("The Cut and Copy commands require an area selection, or no selection").

Any further suggestions would be greatly appreciated, thanks --

David

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[Bill Christens-Barry-2]

David,

If your structures don't overlap spatially, and you can define some minimum separation criterion, then you might create a macro to check that each new selection is far enough from the others. New candidate selections could be nullified if they were too close to existing ones. The downside is that you won't know that every structure in the image has been added until you use the ROI Manager to display all that have been added.

Bill Christens-Barry

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[David Nauen-2]

Thanks for your helpful reply.  Using 't' is much faster than shift add, show all keeps the measurement lines on the image and is thus indispensible, and multi-measure saves a lot of time.

Under Analyze/Set Measurements there are many options but I don't believe there's anything that would return the xy position of the measurement bar.  Hence I still need ROI, but I can't find any straightforward way to copy or export the data (mean x-value and mean y-value of each measurement line) from ROI Manager.

Any thoughts would be greatly appreciated.  Thanks again,
David

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[David Nauen-2]

Thanks for the suggestions.  In case anyone else needs the position (mean x- and y-value) of measurement lines: these values are used as the name of each ROI in ROI Manager.  To export the ROI names, I used More/Save.  This produced a zipped directory containing a file for each x,y pair, with the pair determining the filename, with x- and y-value separated by a hyphen.  After unzipping the directory, from the command line I made the list using  ls *.roi | sed -e s/-/,/ -e s/.roi/\;/ > roilist.txt

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