Re: Reslice stack with a rotated rectangular selection.

Posted by Bill Mohler on
URL: http://imagej.273.s1.nabble.com/Reslice-stack-with-a-rotated-rectangular-selection-tp3692983p3692986.html

AFAIK, input spacing is the number of pixels that should be assumed
to lie between slices in your Z-stack. Output spacing controls how
many pixels to move the reslicing line before taking the next slice
for your new stack.

>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]
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>>
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