(no subject)

[Darrel Snyder]

 

ImageJ list members,

 

I am new to the list and ImageJ program and am not very familiar with the
program.  I would like to draw upon your experience and knowledge for some
suggestions or advice.

 

I study the morphological development of larval and early juvenile fishes
(~2 to 50 mm total length) mostly under a low-powered stereomicroscope or
macrozoom lens.  I hope to use ImageJ (or a free or inexpensive
alternative) and a UBS or firewire camera to inexpensively replace an old
image analysis system based on old BioScan Optimas software, none of which
will work with current pcs and windows operating systems).  My use of ImageJ
at this time would be largely limited to simple enhancement of images,
spatially calibrating the image, making measurements using lines or series
of points for horizontal distances between their coordinates, and
transferring the resultant data to spreadsheets for analysis and
summarization.  Unfortunately, in ImageJ, or among the various plugins and
macros (as listed on the website), I was unable to find any way to:

 

1.                  draw (between or at landmark features or structures),
view, and measure more than one line at a time, preferably with the lines
sequentially numbered for identification and editable (end points adjusted
if necessary), much like for multiple points with reported coordinates;

 

2.                  reset the coordinate origin of the image from the upper
left (from which y values are treated as positive rather than negative-why
and why isn't the default origin in the lower left corner) to some selected
point on the image (if I set the origin at the anterior end of the image of
a fish larva, the x value for points at various landmarks would be the
horizontal length to that point without any further calculation);

 

3.                  modify the results window such that it remains visible
(is not minimized) as additional measurements are made;

 

4.                  modify the results window such that only the measure I
am interested in is displayed and ready to be copied and pasted to my
spreadsheet (e.g., only measurement number and length for line
measurements-angle not wanted, and only point number and x or x and y for
point coordinates-don't need z or value;

 

5.                  have the contents of the results window exported
beginning at the current active cell or a specified cell in my spreadsheet
without having to manually cut and paste.

 

Are there any procedures, plugins, or macros that would allow me to do the
above?  Are there more limited image measurement/analysis freeware or
inexpensive software packages that might better suit my relatively simple
needs?

 

Finally, any recommendations for an inexpensive USB or firewire c-mount
camera (at least 2-3 megapixel) for use with stereomicroscopes and c-mount
macrolens?  One from which images could be acquired directly by ImageJ would
be convenient, but not necessary.

 

Sincerely,

 

Darrel Snyder

Larval Fish Laboratory

Colorado State University

[hidden email]

[Volker Baecker]

Hello,

Darrel Snyder a écrit :
>  
> I am new to the list and ImageJ program

Welcome!

> 1.                  draw (between or at landmark features or structures),
> view, and measure more than one line at a time, preferably with the lines
> sequentially numbered for identification and editable (end points adjusted
> if necessary), much like for multiple points with reported coordinates;

All this is possible using the Roi Manager (Analyze>Tools>Roi Manager).
Click "show all" and create your line selections. The lines are numbered
(1,2,3,...) and you can still modify them. I sometimes need to click
update in the Roi Manager after a modification. It works with segmented
lines as well as with straight lines.


ObjectJ might do what you want as well, but I don't see any news from
this project. Does anyone know what has become of it?

Volker Bäcker

--
passerelle antivirus du campus CNRS de Montpellier
--

[Darrel Snyder]

Volker,

Thank you for responding on my multiple line measurement question question.

I was very optimistic about using the region of interest manager to display,
number, and measure multiple lines drawn on an image.  Unfortunately, I
can't seem to make it work following the steps you suggest (I can still only
draw, view and measure one line at time, although measures for each
successive line measured are displayed in the report window -- are we
missing a step or something else?

Darrel

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Volker
Bäcker
Sent: Friday, February 22, 2008 2:46 AM
To: [hidden email]
Subject:

Hello,

Darrel Snyder a écrit :
>  
> I am new to the list and ImageJ program

Welcome!

> 1.                  draw (between or at landmark features or structures),
> view, and measure more than one line at a time, preferably with the lines
> sequentially numbered for identification and editable (end points adjusted
> if necessary), much like for multiple points with reported coordinates;

All this is possible using the Roi Manager (Analyze>Tools>Roi Manager).
Click "show all" and create your line selections. The lines are numbered
(1,2,3,...) and you can still modify them. I sometimes need to click
update in the Roi Manager after a modification. It works with segmented
lines as well as with straight lines.


ObjectJ might do what you want as well, but I don't see any news from
this project. Does anyone know what has become of it?

Volker Bäcker

--
passerelle antivirus du campus CNRS de Montpellier
--