better line length measurement...

[Nick-2]

Hello.

I am trying to use imagej to measure line widths.  I am quite
comfortable setting the scale and using the line tool to make a
measurement, but I was wondering if there was some way to help guide
the line I draw and make sure that it is perpendicular to the feature.
 For instance, other programs usually have a tool that looks like:
|<------->|
I am really after those vertical lines on the edges (perhaps a bit
longer).  So, if I am measuring the width of a strip, I can align
those vertical lines with the edges of my strip; helping me get more
accurate measurements.

I know that by holding down the shift key I can make the line I draw
perfectly horizontal, but my images may not always be in the proper
orientation.

I also thought that I could use the rectangle tool to make a box and
measure the width and height, though I cannot rotate it...

Any ideas?

[Theresa Swayne]

Hi Nick,

If you double-click on the line tool and change the line width to a  
large enough number you will get a wide semi-transparent shadow on the  
line selection, the ends of which are perpendicular to the line.

Hope this helps,
Theresa


On Mar 23, 2011, at 2:01 PM, Nick wrote:

> I am trying to use imagej to measure line widths.  I am quite
> comfortable setting the scale and using the line tool to make a
> measurement, but I was wondering if there was some way to help guide
> the line I draw and make sure that it is perpendicular to the feature.
> For instance, other programs usually have a tool that looks like:
> |<------->|
> I am really after those vertical lines on the edges (perhaps a bit
> longer).  So, if I am measuring the width of a strip, I can align
> those vertical lines with the edges of my strip; helping me get more
> accurate measurements.

------------------------------------
Theresa C. Swayne, Ph.D.
Manager, Confocal and Specialized Microscopy Shared Resource
Herbert Irving Comprehensive Cancer Center, Columbia University
1130 Saint Nicholas Ave, 222A
New York, NY 10032

212-851-4613

[hidden email]
http://www.hiccc.columbia.edu/research/sharedresources/confocal

[Jim Passmore-2]

Nick,

I've thought of setting up ImageJ to do something similar.  Wayne posted a
macro a while back that measured perpendicular distance to lines.  His
approach began by having user draw a line, then pressing a key to store that
line.  The line stayed selected, and you could simply drag it by grabbing
the center point.  Once it was repositioned, you could press another key to
store the second line.  The process went on from there, but I could see
stopping here and calculating the distance between the lines.

In case you're comfortable mucking around in macro code, I'll attach the
file.  No credit due to me--it was all Wayne.  At some point I'm going to
adapt it to create such a tool, but my application will require creating and
filling in a results table as well.

Hope this gets you started.

*Jim Passmore
*Sealed Air Corporation



On Wed, Mar 23, 2011 at 2:01 PM, Nick <[hidden email]> wrote:

> Hello.
>
> I am trying to use imagej to measure line widths.  I am quite
> comfortable setting the scale and using the line tool to make a
> measurement, but I was wondering if there was some way to help guide
> the line I draw and make sure that it is perpendicular to the feature.
>  For instance, other programs usually have a tool that looks like:
> |<------->|
> I am really after those vertical lines on the edges (perhaps a bit
> longer).  So, if I am measuring the width of a strip, I can align
> those vertical lines with the edges of my strip; helping me get more
> accurate measurements.
>
> I know that by holding down the shift key I can make the line I draw
> perfectly horizontal, but my images may not always be in the proper
> orientation.
>
> I also thought that I could use the rectangle tool to make a box and
> measure the width and height, though I cannot rotate it...
>
> Any ideas?
>

[Cammer, Michael]

This sounds like something I wrote years ago (and please don't ask me to dig up the code from 2004 maybe) to calculate the distance of endocytic vesicles inside cells to the surface of the cell.  The cells were very bright fluorescent protein so each slice of a confocal Z stack was thresholded, selected, and the XY coordinates of the ROI from each slice were stored.  Then the user clicked on each vesicle and these XYZ center coordinates were stored in an array.  Then the distance from each vesicle to each point on the 3D border was calculated to find the shortest distance for each.  It was inelegant brute force but worked.  Instead of reporting distance, you could report the coordinates to define the perpendicular.
_________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]

________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of Jim Passmore [[hidden email]]
Sent: Thursday, March 24, 2011 10:39 PM
To: [hidden email]
Subject: Re: better line length measurement...

Nick,

I've thought of setting up ImageJ to do something similar.  Wayne posted a
macro a while back that measured perpendicular distance to lines.  His
approach began by having user draw a line, then pressing a key to store that
line.  The line stayed selected, and you could simply drag it by grabbing
the center point.  Once it was repositioned, you could press another key to
store the second line.  The process went on from there, but I could see
stopping here and calculating the distance between the lines.

In case you're comfortable mucking around in macro code, I'll attach the
file.  No credit due to me--it was all Wayne.  At some point I'm going to
adapt it to create such a tool, but my application will require creating and
filling in a results table as well.

Hope this gets you started.

*Jim Passmore
*Sealed Air Corporation

------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================

[Cammer, Michael]

It should say, the edge coordinates, not all coordinates...

_________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]

________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of Cammer, Michael [[hidden email]]
Sent: Thursday, March 24, 2011 11:03 PM
To: [hidden email]
Subject: Re: better line length measurement...

This sounds like something I wrote years ago (and please don't ask me to dig up the code from 2004 maybe) to calculate the distance of endocytic vesicles inside cells to the surface of the cell.  The cells were very bright fluorescent protein so each slice of a confocal Z stack was thresholded, selected, and the XY coordinates of the ROI from each slice were stored.  Then the user clicked on each vesicle and these XYZ center coordinates were stored in an array.  Then the distance from each vesicle to each point on the 3D border was calculated to find the shortest distance for each.  It was inelegant brute force but worked.  Instead of reporting distance, you could report the coordinates to define the perpendicular.
_________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]

________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of Jim Passmore [[hidden email]]
Sent: Thursday, March 24, 2011 10:39 PM
To: [hidden email]
Subject: Re: better line length measurement...

Nick,

I've thought of setting up ImageJ to do something similar.  Wayne posted a
macro a while back that measured perpendicular distance to lines.  His
approach began by having user draw a line, then pressing a key to store that
line.  The line stayed selected, and you could simply drag it by grabbing
the center point.  Once it was repositioned, you could press another key to
store the second line.  The process went on from there, but I could see
stopping here and calculating the distance between the lines.

In case you're comfortable mucking around in macro code, I'll attach the
file.  No credit due to me--it was all Wayne.  At some point I'm going to
adapt it to create such a tool, but my application will require creating and
filling in a results table as well.

Hope this gets you started.

*Jim Passmore
*Sealed Air Corporation

------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================

------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================