[ome-users] User Guides Website Feedback

Fri Feb 21 18:36:05 GMT 2014

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<mailto:peter.z.gerondelis at gsk.com>
Mobile  +19192254432
Tel       +19194831171

gsk.com<http://www.gsk.com/>  |  Twitter<http://twitter.com/GSK>  |  YouTube<http://www.youtube.com/user/gskvision>  |  Facebook<http://www.facebook.com/glaxosmithkline>  |  Flickr<http://www.flickr.com/photos/glaxosmithkline>

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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-formats.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<mailto: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:

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Amersham .gel file warning<https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;9ad542ec.0512>

From:

<image001.png>

Morri Feldman <[log in to unmask]<https://list.nih.gov/cgi-bin/wa.exe?LOGON=A2%3Dind0512%26L%3DIMAGEJ%26P%3DR16807%261%3DIMAGEJ%269%3DA%26I%3D-3%26J%3Don%26d%3DNo%2BMatch%253BMatch%253BMatches%26z%3D4>>

Reply-To:

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ImageJ Interest Group <[log in to unmask]<https://list.nih.gov/cgi-bin/wa.exe?LOGON=A2%3Dind0512%26L%3DIMAGEJ%26P%3DR16807%261%3DIMAGEJ%269%3DA%26I%3D-3%26J%3Don%26d%3DNo%2BMatch%253BMatch%253BMatches%26z%3D4>>

Date:

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Tue, 20 Dec 2005 11:54:00 -0800

Content-Type:

<image001.png>

text/plain

Parts/Attachments:

<image001.png>

<image002.png>

text/plain<https://list.nih.gov/cgi-bin/wa.exe?A3=ind0512&L=IMAGEJ&E=8bit&P=698804&B=--&T=text%2Fplain;%20charset=ISO-8859-1&header=1> (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/1F801602120AE332C1256EB400484111?OpenDocument&querytitle=&hometitle=search

A pdf document from when Molecular Dynamics owned the .gel file format:

http://research.stowers-institute.org/efg/ScientificSoftware/Utility/TiffTags/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<mailto:peter.z.gerondelis at gsk.com>
Mobile  +19192254432
Tel       +19194831171

gsk.com<http://www.gsk.com/>  |  Twitter<http://twitter.com/GSK>  |  YouTube<http://www.youtube.com/user/gskvision>  |  Facebook<http://www.facebook.com/glaxosmithkline>  |  Flickr<http://www.flickr.com/photos/glaxosmithkline>

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