Re: Reslice stack with a rotated rectangular selection.

Posted by Michael Cundell on
URL: http://imagej.273.s1.nabble.com/Reslice-stack-with-a-rotated-rectangular-selection-tp3692983p3692985.html

Thanks so much Bill,

You just saved me many many hours and that was so so simple.  It does raise
one last question.  What is the input Z spacing and output Z spacing?  I can
see the effects if I change those figures for myself but i dont understand
what they are doing.  The default for my image is 0.3um for both, but im not
sure if this is just some kind of image J default or a default that is
calculated from the image i open?  Really the most important question is
that im not sure what value is biologically relevent to my microscope
image/cells, or whether there even is a biolgically relevent value i should
be setting those parameters at?  I dont want to unknowingly end up
manipulating my data by setting parameters that I have no idea what they are
actually doing and then not being able to explain myself.

Any help from anyone on this would be appreciated.

Mike

----- Original Message -----
From: "Bill Mohler" <[hidden email]>
To: <[hidden email]>
Sent: Saturday, April 11, 2009 9:10 PM
Subject: Re: Reslice stack with a rotated rectangular selection.

> You should experiment with reslicing from a line selection. You can start
> from any angle, and then define how far you want the slicing to progress
> orthogonally.
>
>>Hey,
>>
>>Is there a plugin that will let me use the reslice command with a
>>rectangular selection that I have rotated using edit>selection>rotate.
>>When you rotate a rectangular selection reslice does not work anymore
>>saying "line or rectangular selection required".
>>
>>The object im reslicing needs to be horizontal, and then i perform reslice
>>from the top on my stack.  I have about 50 cells im reslicing per field of
>>view but all the cells are all at different angles.  Currently im having
>>to rotate my image constantly using image>rotate, getting each object im
>>reslicing within the cell horizontal, then reslicing from the top with a
>>normal rectangular selection.  Im using interpolation when rotating my
>>image.  Is using interpolation and rotating many times a bad thing? the
>>object im looking at after reslicing is only about 1.5 microns in diameter
>>and is relatively close to the microscopes Z-sectioning/camera resolution.
>>
>>I should also say that i dont use imageJ extensively, and I do not know
>>how to code, so if there is any options for what im trying to do Lehman's
>>terms would be much appreciated.
>>
>>Thanks !
>
>
> --
> -----------------
> William A. Mohler
> Associate Professor
> Dept. of Genetics and Developmental Biology
> University of Connecticut Health Center
> MC-3301
> 263 Farmington Ave.
> Farmington, CT   06030-3301
>
> [hidden email]
> Mobile: [phone]
> alt. mobile: [phone]
> skype: wmohler
>
> Office: [phone], room E2029
> Lab: [phone], room E2032
> Fax: [phone]
>
> G&DB dept. ofc.: [phone]
> G&DB dept. fax : [phone]
> http://genetics.uchc.edu/Faculty/Mohler/Mohler.html
>