Reslice stack with a rotated rectangular selection.

[Michael Cundell]

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 !

[Bill Mohler]

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

[Michael Cundell]

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
>

[Bill Mohler]

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

[Michael Cundell]

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
>