Writing Pixel Calibration to Tiff File
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Writing Pixel Calibration to Tiff File
 
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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 -- *Cameron J. Nowell* Head Imaging, FACS and Analysis Core Monash Institute of Pharmaceutical Sciences Monash University 399 Royal Parade Parkville, VIC, 3052 Australia *Email:* [hidden email] *Phone: *+61 422882700 *LinkedIn: *Profile <http://au.linkedin.com/pub/cameron-nowell/23/57/884/> *Research Gate: * Profile <http://www.researchgate.net/profile/Cameron_Nowell> *Google Scholar:* Profile <https://scholar.google.com/citations?user=qqQfgZIAAAAJ&hl=en> *PubMed Bibliography: *Profile <http://www.ncbi.nlm.nih.gov/sites/myncbi/1TK3WeparcvQr/bibliography/47922177/public/?sort=date&direction=ascending> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Writing Pixel Calibration to Tiff File
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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 > > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Writing Pixel Calibration to Tiff File
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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 >> >> >> > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- *Cameron J. Nowell* Head Imaging, FACS and Analysis Core Monash Institute of Pharmaceutical Sciences Monash University 399 Royal Parade Parkville, VIC, 3052 Australia *Email:* [hidden email] *Phone: *+61 422882700 *LinkedIn: *Profile <http://au.linkedin.com/pub/cameron-nowell/23/57/884/> *Research Gate: * Profile <http://www.researchgate.net/profile/Cameron_Nowell> *Google Scholar:* Profile <https://scholar.google.com/citations?user=qqQfgZIAAAAJ&hl=en> *PubMed Bibliography: *Profile <http://www.ncbi.nlm.nih.gov/sites/myncbi/1TK3WeparcvQr/bibliography/47922177/public/?sort=date&direction=ascending> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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