[ome-users] User Guides Website Feedback

Tue Feb 25 23:21:40 GMT 2014

Melissa,  Terrific!  Thank you very much for the explanation.  While I took AP computer science in high school I didn't learn anything beyond Pascal so I can't decipher the source code!!  However, if you say that Bioformats corrects for it so that it can be properly quantitated with ImageJ, then it sounds like you guys have collectively (ImageJ and Bioformats) developed a replacement for the Molecular Dynamics/Amersham/GE Healthcare ImageQuant software and I suppose much more.  Thank you so much!

BTW, thx for directing me to the INVERT LUT function.  Best, Pete

Peter Gerondelis, Ph.D.
S Investigator
HIV DPU
RD Infectious Disease R&D

GSK
5 Moore Drive, PO Box 13398, RTP, NC 27709-3398, United States
Email	peter.z.gerondelis at gsk.com
Mobile	+19192254432
Tel	+19194831171

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-----Original Message-----
From: Melissa Linkert [mailto:melissa at glencoesoftware.com] 
Sent: Monday, February 24, 2014 7:26 PM
To: Peter Gerondelis
Cc: Helen Flynn; <ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] User Guides Website Feedback

Hi Pete,

> All, I looked at these very helpful links and information.  Managed to install the 'loci-tools.jar' file and imported a .gel file.  So I noticed that unlike opening directly, the image is inverted (black background with white/grey data).  Any way to flip this around.
>

The "Image > Lookup Tables > Invert LUT" option in ImageJ should cause the minimum pixel value to be shown as white instead of black.

> More importantly, does the software correct for the transformation to enable proper quantitation of the data?  I read the technical document:
>
>
>
> http://www.awaresystems.be/imaging/tiff/tifftags/docs/gel.html
>
>
>
> While helpful I don't understand it fully (I'm a virologist/biochemists).  I also can't tell whether the recommendation of the writer ("The data should be decoded like this: grayscale_value - Square (stored_value)*scale) has actually been implemented.
>

Yes, the pixel values shown on screen are calculated as
square(stored_value) * scale.  If you are curious, the relevant source code is:

https://github.com/openmicroscopy/bioformats/blob/dev_5_0/components/formats-gpl/src/loci/formats/in/GelReader.java#L122

Note that ImageJ itself does not perform this correction, so the image shown when opening the file without Bio-Formats contains the raw stored values.

Regards,
-Melissa

On Fri, Feb 21, 2014 at 12:36 PM, Peter Gerondelis <peter.z.gerondelis at gsk.com> wrote:
>
> Thank you Helen.  I really appreciate the availability of these resources thank you.
>
>
>
> All, I looked at these very helpful links and information.  Managed to install the 'loci-tools.jar' file and imported a .gel file.  So I noticed that unlike opening directly, the image is inverted (black background with white/grey data).  Any way to flip this around.
>
>
>
> More importantly, does the software correct for the transformation to enable proper quantitation of the data?  I read the technical document:
>
>
>
> http://www.awaresystems.be/imaging/tiff/tifftags/docs/gel.html
>
>
>
> While helpful I don't understand it fully (I'm a 
> virologist/biochemists).  I also can't tell whether the recommendation 
> of the writer ("The data should be decoded like this: grayscale_value 
> - Square (stored_value)*scale) has actually been implemented.  If so, 
> then this is terrific.  I will be free of ImageQuant forever and will 
> pass this on to other biochemists I know.  Best, Pete
>
>
>
> Peter Gerondelis, Ph.D.
>
> S Investigator
>
> HIV DPU
>
> RD Infectious Disease R&D
>
>
>
> GSK
>
> 5 Moore Drive, PO Box 13398, RTP, NC 27709-3398, United States
>
> Email   peter.z.gerondelis at gsk.com
>
> Mobile  +19192254432
>
> Tel       +19194831171
>
>
>
> gsk.com  |  Twitter  |  YouTube  |  Facebook  |  Flickr
>
>
>
>
>
> From: Helen Flynn [mailto:h.flynn at dundee.ac.uk]
> Sent: Friday, February 21, 2014 1:15 PM
> To: Peter Gerondelis
> Cc: <ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: User Guides Website Feedback
>
>
>
> Dear Peter,
>
>
>
> I am replying cc'd to our users list which is the proper place to ask Bio-Formats related questions.
>
>
>
> The information on what formats Bio-Formats supports is on
>
> http://www.openmicroscopy.org/site/support/bio-formats5/supported-form
> ats.html
>
>
>
> If you click on the format type you have in this table, you will find more information about how well each format is supported which should answer your question about the transformation.
>
>
>
> We are hoping to release an updated version of the Bio-Formats plugin 
> early next week but in the meantime, you can download the 
> 'loci-tools.jar' from 
> http://downloads.openmicroscopy.org/bio-formats/5.0.0-rc1/
>
> and use the documentation on http://www.openmicroscopy.org/site/support/bio-formats5/users/imagej/installing.html and http://www.openmicroscopy.org/site/support/bio-formats5/users/imagej/load-images.html to guide you through getting it installed and loading your images.
>
>
>
> If you need any further help, please reply to the mailing list and 
> someone will get back to you next week,
>
>
>
> Thanks,
>
>
>
> Helen
>
>
>
>
>
>
>
> On 21 Feb 2014, at 17:53, Peter Gerondelis <peter.z.gerondelis at gsk.com> wrote:
>
>
>
> Thank you for contacting us.
> Please provide as much information as possible so we can deal with your enquiry efficiently.
>
>
>
> Hi, I am looking to use ImageJ to analyze phosphorimaging files from my Typhoon and Storm.  I can no longer use the software provided by the manufacturer (formerly Molecular Dynamics, then Amersham and now GE).  My understanding is that these are not ordinary TIFF files.  They are transformed by the instrument and/or software. Someone from the ImageJ list serve suggested that I try Bio Formats plugin.  I thought I would try it but can't figure out how to install.  Before I put any additional energy to getting this plugin and installing it, I would like to confirm that the plugin does more than just open the file, but does it handle the transformation correctly?  If so, can you explain to me which file I need to download from the website, how to get it properly installed into ImageJ and how to use it????
>
> Please note the following related post from the ImageJ list serve:
>
>
>
>
>
>
>
> Subject:
>
> <image001.png>
>
> Amersham .gel file warning
>
> From:
>
> <image001.png>
>
> Morri Feldman <[log in to unmask]>
>
> Reply-To:
>
> <image001.png>
>
> ImageJ Interest Group <[log in to unmask]>
>
> Date:
>
> <image001.png>
>
> Tue, 20 Dec 2005 11:54:00 -0800
>
> Content-Type:
>
> <image001.png>
>
> text/plain
>
> Parts/Attachments:
>
> <image001.png>
>
> <image002.png>
>
> text/plain (29 lines)
>
> The Amersham .gel file format is based on the tiff standard.  ImageJ
>
> will read .gel files because they are tiff files.  Unfortunately
>
> Amersham scanners (e.g. Typhoon and Storm) transform the original
>
> pixel values by taking their square root and scaling them before
>
> saving them to a .gel file.  When imagej opens a .gel file, it doesn't
>
> reverse this transformation making the images appear muted and
>
> unsuitable for quantification.
>
>
>
> Here are some links.
>
>
>
> A short note about Amersham's .gel file format:
>
> http://www4.amershambiosciences.com/aptrix/upp00919.nsf/content/1F8016
> 02120AE332C1256EB400484111?OpenDocument&querytitle=&hometitle=search
>
>
>
> A pdf document from when Molecular Dynamics owned the .gel file format:
>
> http://research.stowers-institute.org/efg/ScientificSoftware/Utility/T
> iffTags/GEL-FileFormat.pdf
>
>
>
> If the information in the pdf is current, it should be possible to
>
> read a few private tiff tags from the .gel file and use their values
>
> to reverse the image transformation.  Barring this solution, be wary
>
> of quantifying data directly from .gel files.
>
>
>
> Best,
>
> Morri
>
>
>
> --
>
> Morri Feldman
>
> (415) 514-0575
>
> Shokat Lab
>
> UCSF Biophysics Program
>
> Best, Pete
>
>
>
> Peter Gerondelis, Ph.D.
>
> S Investigator
>
> HIV DPU
>
> RD Infectious Disease R&D
>
>
>
> GSK
>
> 5 Moore Drive, PO Box 13398, RTP, NC 27709-3398, United States
>
> Email   peter.z.gerondelis at gsk.com
>
> Mobile  +19192254432
>
> Tel       +19194831171
>
>
>
> gsk.com  |  Twitter  |  YouTube  |  Facebook  |  Flickr
>
>
>
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>
>
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>
>
>
>
>
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