Re: Reslice stack with a rotated rectangular selection.

Posted by Michael Cundell on Apr 12, 2009; 1:35am
URL: http://imagej.273.s1.nabble.com/Reslice-stack-with-a-rotated-rectangular-selection-tp3692983p3692987.html

rather than pixels I think the input and output are based on the distance
between pixels rather than actual pixel numbers as the units are microns?

The file I am opening is a deltavision file.  I have used the manufacturers
own software (softworx explorer) and measured from one pixel to the next and
it comes out at 0.1103 microns.  Im guessing for a 1:1 representation of a
biological structure in my reslice in imageJ I should set input and output Z
spacing to 0.1103 microns?  but then how does imageJ know what the distance
between two of the pixels in my image actually is?  I guess this information
is saved in the deltavision file itself?  I have just previously been using
the default 0.3 micron spacing when reslicing.  I guess It doesnt make so
much difference, it just squashes/stretches the output image slightly.


----- Original Message -----
From: "Bill Mohler" <[hidden email]>
To: <[hidden email]>
Sent: Saturday, April 11, 2009 9:48 PM
Subject: Re: Reslice stack with a rotated rectangular selection.

> 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]
>>>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
>