Is meta data correct for imageJ sample image confocal-series.tif???

[Daniel White]

Hi Joel,

Firstly,  thanks for providing the
confocal-series.tif
test image to the imageJ community!

I have a question about the image's meta data, seen below, from ImageJ/Fiji
"Show Info..."

It's a confocal stack, so xy pixel spacing of 54.5 nm is at the lower limit
for 1.4 NA imaging, which is good.
But the z slice spacing, also of 54.5 nm seems incorrect perhaps?
Should It really be more like 200 nm or 250 nm or so?

Should we correct the meta data in the imageJ sample data file if its
wrong?


cheers

Dan





Cells double labeled with P53-YFP and Mito-Red imaged on a
Leica SP1 confocal microscope.  Original series cropped from
512x512 pixels to 400x400.  The green channel was subjected
to one round of smoothing. Image is courtesy of Joel Sheffield.

------------------------------------------------------
(Fiji Is Just) ImageJ 2.0.0-rc-54/1.51g; Java 1.8.0_45 [64-bit]; Windows 7
6.1; 544MB of 6040MB (9%)

Title: confocal-series.tif
Width:  21.7820 µm (400)
Height:  21.7820 µm (400)
Depth:  1.3614 µm (25)
Size:  7.6MB
Resolution:  18.3638 pixels per µm
Voxel size: 0.0545x0.0545x0.0545 µm^3
ID: -332
Bits per pixel: 8 (grayscale LUT)
Display ranges
  1: 0-230
  2: 0-208
Image: 1/50
  Channel: 1/2
  Slice: 1/25
  Composite mode: "composite"
No threshold
Uncalibrated
URL: http://imagej.nih.gov/ij/images/confocal-series.zip
Screen location: 514,150 (1366x768)
Coordinate origin:  0,0,0
No overlay
No selection

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[Joel Sheffield]

Thank you for pointing this out to me.  I'm frankly a little puzzled about
the error, but I've checked the original, and the slice spacing is supposed
to 0.6 micron.  For the 25 sections, then, the overall depth should be 15
micron.  Please do modify the file data.



Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  *http://tinyurl.com/khbouft <http://tinyurl.com/khbouft>*

On Mon, Nov 7, 2016 at 7:46 AM, Daniel White <[hidden email]> wrote:

> Hi Joel,
>
> Firstly,  thanks for providing the
> confocal-series.tif
> test image to the imageJ community!
>
> I have a question about the image's meta data, seen below, from
> ImageJ/Fiji "Show Info..."
>
> It's a confocal stack, so xy pixel spacing of 54.5 nm is at the lower
> limit for 1.4 NA imaging, which is good.
> But the z slice spacing, also of 54.5 nm seems incorrect perhaps?
> Should It really be more like 200 nm or 250 nm or so?
>
> Should we correct the meta data in the imageJ sample data file if its
> wrong?
>
>
> cheers
>
> Dan
>
>
>
>
>
> Cells double labeled with P53-YFP and Mito-Red imaged on a
> Leica SP1 confocal microscope.  Original series cropped from
> 512x512 pixels to 400x400.  The green channel was subjected
> to one round of smoothing. Image is courtesy of Joel Sheffield.
>
> ------------------------------------------------------
> (Fiji Is Just) ImageJ 2.0.0-rc-54/1.51g; Java 1.8.0_45 [64-bit]; Windows 7
> 6.1; 544MB of 6040MB (9%)
>
> Title: confocal-series.tif
> Width:  21.7820 µm (400)
> Height:  21.7820 µm (400)
> Depth:  1.3614 µm (25)
> Size:  7.6MB
> Resolution:  18.3638 pixels per µm
> Voxel size: 0.0545x0.0545x0.0545 µm^3
> ID: -332
> Bits per pixel: 8 (grayscale LUT)
> Display ranges
>   1: 0-230
>   2: 0-208
> Image: 1/50
>   Channel: 1/2
>   Slice: 1/25
>   Composite mode: "composite"
> No threshold
> Uncalibrated
> URL: http://imagej.nih.gov/ij/images/confocal-series.zip
> Screen location: 514,150 (1366x768)
> Coordinate origin:  0,0,0
> No overlay
> No selection
>
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Rasband, Wayne (NIH/NIMH) [E]]

> On Nov 10, 2016, at 11:24 AM, JOEL B. SHEFFIELD <[hidden email]> wrote:
>
> Thank you for pointing this out to me.  I'm frankly a little puzzled about the error, but I've checked the original, and the slice spacing is supposed to 0.6 micron.  For the 25 sections, then, the overall depth should be 15 micron.  Please do modify the file data.

Thanks Joel. I changed the slice spacing of the Confocal Series sample image to 0.6 microns. The Image>Stacks>Orthogonal Views and Image>Stacks>3 D Project commands now work much better. You will need to delete ImageJ/samples/confocal-series.zip if you have used the File>Open Samples>Cache Sample Images command.

-wayne

> On Mon, Nov 7, 2016 at 7:46 AM, Daniel White <[hidden email]> wrote:
> Hi Joel,
>
> Firstly,  thanks for providing the
> confocal-series.tif
> test image to the imageJ community!
>
> I have a question about the image's meta data, seen below, from ImageJ/Fiji "Show Info..."
>
> It's a confocal stack, so xy pixel spacing of 54.5 nm is at the lower limit for 1.4 NA imaging, which is good.
> But the z slice spacing, also of 54.5 nm seems incorrect perhaps?
> Should It really be more like 200 nm or 250 nm or so?  
>
> Should we correct the meta data in the imageJ sample data file if its wrong?
>
>
> cheers
>
> Dan
>
>
>
>
>
> Cells double labeled with P53-YFP and Mito-Red imaged on a  
> Leica SP1 confocal microscope.  Original series cropped from
> 512x512 pixels to 400x400.  The green channel was subjected
> to one round of smoothing. Image is courtesy of Joel Sheffield.
>
> ------------------------------------------------------
> (Fiji Is Just) ImageJ 2.0.0-rc-54/1.51g; Java 1.8.0_45 [64-bit]; Windows 7 6.1; 544MB of 6040MB (9%)
>  
> Title: confocal-series.tif
> Width:  21.7820 µm (400)
> Height:  21.7820 µm (400)
> Depth:  1.3614 µm (25)
> Size:  7.6MB
> Resolution:  18.3638 pixels per µm
> Voxel size: 0.0545x0.0545x0.0545 µm^3
> ID: -332
> Bits per pixel: 8 (grayscale LUT)
> Display ranges
>   1: 0-230
>   2: 0-208
> Image: 1/50
>   Channel: 1/2
>   Slice: 1/25
>   Composite mode: "composite"
> No threshold
> Uncalibrated
> URL: http://imagej.nih.gov/ij/images/confocal-series.zip
> Screen location: 514,150 (1366x768)
> Coordinate origin:  0,0,0
> No overlay
> No selection
>
>

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