Line profiles not embedding when saving .TIF

zstamplis

Hi there,

I've been using Image-Pro 11 to do some image analysis/annotation on juvenile fish otoliths. I primarily utilize the line profile function to mark daily growth increments on transect lines.  Other colleagues have shared .TIF files with me that have line profiles embedded into the image and they appear no problem when opened in Image-Pro 11.  However, every time I've attempted to save an image that I've added line profiles to (through the file - save as option) they disappear.  The only workaround right now is to save separate .lpf files in the Line Profile tool, but this is tedious when working with hundreds of images and I know in previous versions of Image Pro this worked just fine.  I've checked the settings window extensively and there appear to be at least two or three different options for saving line profiles (I've tried basically every combination of turning them on and off to no avail) . Is there something simple I'm missing?  Thanks for any help!  Unsure if this matters but all images were captured on a Nikon Eclipse TI-2 microscope via Nikon Elements.  I'm using Image-Pro 2D Measurements - v11.0 Module

CraigW

Upon investigation we see that the problem is caused by the way that we preserve the Description TIFF tag when opening an OME-TIFF single frame image.  This causes the saved TIF file to still be interpreted as an OME-TIFF file when it is reloaded which bypasses loading of the line-profile data.  We will fix this in the upcoming ll.1.1 patch release, but I have a workaround for you.

After opening one of these OME-TIFF images, you just need to erase or replace the Image Description property.  You can do this interactively from the Document Properties (the blue oval with "i" in it in the image context panel).  In the Document Properties "Metadata" template, you will find the Description property as shown below:

Just replace the Description with nothing or some other text (other than the OME-TIFF header, of course).

Alternately you can just run this little macro which will empty out the Description property of the ActiveImage

    Public Sub ClearDescription()
        ThisApplication.ActiveImage.Description = ""
    End Sub

After replacing or clearing the description, your line profile will be saved when you save the image as a TIFF file, and will be available when you open the Line Profile panel after opening that saved tiff file.

NikitaRG

Hi zstamplis,

Please verify "Save Line Profile" option is checked (Histogram & Profile page, Line Profile section). The complete information of the line profile tool saved with the .tif images.
Could you please attach an example image for future investigation?

Thanks,
Nikita.

zstamplis

Hi Nikita,

I've attached some screenshots of my setup below as well as an example .TIF I've been using (cropped since these files are huge in their full format).  I've changed the initial profile setting to all options (none, default, selected and all) with no change.  "None" displays no line profile when loading an image, "default" loads a horizontal line with every image I open, "selected" shows no profiles, and "all" displays the line profile from the last image saved without any of the manual marks saved.  



Thanks for getting back to me!  Hopefully it's just something funky on my setup end.

zstamplis

For some weird added context, it appears that line profiles save okay on some older .TIF images I took with the same microscope and software.  Nikon Elements has a huge list of metadata options you can save into a .TIF as well as an option for "OME" .  One image I was able to save the line profile too was a non-OME TIF (attached below and cropped).  I had some issues getting these OME images to open previously with Image-Pro (~a year ago) but that issue seems to have resolved itself.  

NikitaRG

zstamplis,

Thank you for detailed report. I can reproduce the issue you describing.
17profile.tif (km3e51x25jd8.tif) doesn't save line profile into file, also ROIs and Annotations also fail to save.

2020_01_016_60x(enhanced)_ (egdxd4eowft1.tif)  saves line profile, ROIs and Annotations.
I suspect, this is related to OEM/non-OEM file format and I'll send these images for future investigation.

Last question: what's the version of Image-Pro 11 you are using 11.0.0-11.0.4?

Thanks,
Nikita.

zstamplis

I was running on 11.0.3 but decided to update just in case.  For the time being I'll save all new images as non-OME and convert my old images in Nikon Elements, glad to have at least figured out what is going on and now know it's possibly a filetype issue.  Hoping somewhere down the line this can be fixed!

zstamplis

CraigW said:

Upon investigation we see that the problem is caused by the way that we preserve the Description TIFF tag when opening an OME-TIFF single frame image.  This causes the saved TIF file to still be interpreted as an OME-TIFF file when it is reloaded which bypasses loading of the line-profile data.  We will fix this in the upcoming ll.1.1 patch release, but I have a workaround for you.

After opening one of these OME-TIFF images, you just need to erase or replace the Image Description property.  You can do this interactively from the Document Properties (the blue oval with "i" in it in the image context panel).  In the Document Properties "Metadata" template, you will find the Description property as shown below:

Just replace the Description with nothing or some other text (other than the OME-TIFF header, of course).

Alternately you can just run this little macro which will empty out the Description property of the ActiveImage

    Public Sub ClearDescription()
        ThisApplication.ActiveImage.Description = ""
    End Sub

After replacing or clearing the description, your line profile will be saved when you save the image as a TIFF file, and will be available when you open the Line Profile panel after opening that saved tiff file.

Thanks for getting a manual and macro fix for this so quickly! Seems like an easy enough work around for now and allows me to retain needed metadata including the lens spatial calibration for measurements.