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Re: Writing Pixel Calibration to Tiff File

Posted by Cameron Nowell-3 on Oct 16, 2017; 11:59pm
URL: http://imagej.273.s1.nabble.com/Writing-Pixel-Calibration-to-Tiff-File-tp5019543p5019551.html

Awesome, thanks


On 16 October 2017 at 22:28, Michael Schmid <[hidden email]> wrote:

> Hi Cameron,
>
> you get more information about a tiff file if you select 'Debug mode' in
> Edit>Options>Misc and open a tiff file.
> Then you will see that there is an 'Image Description' which is plain text
> and stored under the tiff tag 270, IMAGEDESCRIPTION
>
> Example 'Image Description' (for an image with x, y units 'nm' and pixel
> value units 'pm':
> ImageJ=1.51p unit=nm vunit=pm min=-136.18 max=274.05
>
> From the JavaDoc of ij.io.TiffDecoder.java:
>
> /** Save the image description in the specified FileInfo. ImageJ
> saves spatial and density calibration data in this string. For
> stacks, it also saves the number of images to avoid having to
> decode an IFD for each image. */
>   public void saveImageDescription
>
> ImageJ will interpret the 'Image Description' only for files written by
> ImageJ.
>
> For writing tiffs by other software, I would recommend to set a
> calibration in centimeters. You can then use the
> setOption("ConvertToMicrons",boolean) macro function in your
> StartupMacros. When this option is set, units in TIFF images are converted
> to microns if the pixel width is less than 0.0001 cm.
>
> Michael
> ________________________________________________________________
> On 16/10/2017 11:15, Cameron Nowell wrote:
>
>> Howdy,
>>
>> I have been hunting around and generally getting more confused.
>>
>> Does anyone know where/how the calibration info is saved into a tiff file
>> from either outside imagej or within? The tiff standard doesn't seem to
>> allow a micron calibration yet it obviously works.
>>
>> Would like to get some custom hardware and software writing out properly
>> calibrated tiff images.
>>
>> Thanks
>>
>> Cam
>>
>>
>>
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