Pixel size for confocal microscopy

[bluebug]

I am confused as to how to get the pixel size for processing a z stack from a SP5 Leica CLSM for use in  another program.

Confocal experiment data:
Magn: 63 x
Dimensions = x 1024
                  y 1024
                  z 33
                   Physical Length                              Physical Origin
                   246.03µm                                     0.00 µm
                   246.03µm                                     0.00 µm
                   -15.81 µm                                    1154.90 µm

[Lloyd Donaldson]

You need to look further down the properties page to voxel width, height, and depth, not the image size values you are looking at. Alternatively you can divide the physical width by the number of pixels etc.


Dr Lloyd Donaldson

Senior Scientist, Project Leader - Microscopy/Wood Identification
Scion - Forests . Products . Innovation
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New Zealand

Ph: 64 7 343 5581
www.scionresearch.com



-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of bluebug
Sent: Saturday, 8 October 2011 5:23 a.m.
To: [hidden email]
Subject: Pixel size for confocal microscopy

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I am confused as to how to get the pixel size for processing a z stack from a
SP5 Leica CLSM for use in  another program.

Confocal experiment data:
Magn: 63 x
Dimensions = x 1024
                  y 1024
                  z 33
                   Physical Length                              Physical
Origin
                   246.03µm                                     0.00 µm
                   246.03µm                                     0.00 µm
                   -15.81 µm                                    1154.90 µm


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[Alberto Diaspro]

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Dear friends,
please have a check here

http://www.nature.com/nmeth/journal/vaop/ncurrent/abs/nmeth.1744.html


All the best
Alby
Alberto Diaspro
Genoa, Italy

[bluebug]

Thank you for your post. Can I just check that this is correct I divided the physical width 246.03µm by 1024  so the pixel size is 0.24µm.
When you referred to the voxels would it be more accurate to use these units? Or how would I use these units?
 


Size-Width 246.0  µm  
Size-Height 246.0  µm  
Size-Depth 15.8 µm
StepSize 0.49  µm  
Voxel-Width 240.5  nm  
Voxel-Height 240.5  nm  
Format-Width 1024  pixels  
Format-Height 1024  pixels  

[bluebug]

Thank you for the link to the paper much appreciated

[Lloyd Donaldson]

The value you calculated 0.24 µm is equivalent to the voxel width of 240 nm, they are the same measurement.

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of bluebug
Sent: Monday, 10 October 2011 12:03 p.m.
To: [hidden email]
Subject: Re: Pixel size for confocal microscopy

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Thank you for your post. Can I just check that this is correct I divided the
physical width 246.03µm by 1024  so the pixel size is 0.24µm.
When you referred to the voxels would it be more accurate to use these
units? Or how would I use these units?



Size-Width 246.0  µm
Size-Height 246.0  µm
Size-Depth 15.8 µm
StepSize 0.49  µm
Voxel-Width 240.5  nm
Voxel-Height 240.5  nm
Format-Width 1024  pixels
Format-Height 1024  pixels



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This e-mail and any attachments may contain information which is confidential or subject to copyright. If you receive this e-mail in error, please delete it.
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[bluebug]

Thanks for the help