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Source for Spectral Image Data

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Blair Rossetti

Source for Spectral Image Data

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Hi Friends,

I am hoping to get access to some spectral microscopy data sets for testing purposes. Ideally, I would like to aggregate a few spectral images from different platforms and file formats. I've checked the Cell Image Library and the repos listed on https://imagej.net/Public_data_sets , but it seems that spectral data sets are scarce on the web. I would greatly appreciate if someone could point me in the right direction.

Thanks!
Blair

Maria Y. Boulina

Re: Source for Spectral Image Data

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi Friends,
>
> I am hoping to get access to some spectral microscopy data sets for
> testing purposes. Ideally, I would like to aggregate a few spectral images
> from different platforms and file formats. I've checked the Cell Image
> Library and the repos listed on https://imagej.net/Public_data_sets , but
> it seems that spectral data sets are scarce on the web. I would greatly
> appreciate if someone could point me in the right direction.
>
> Thanks!
> Blair
>

George McNamara

Re: Source for Spectral Image Data

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Hi Marcia,

Thanks. A Leica SP8 confocal was recently installed in the core I manage
here, so I may be able to help.

Of course YOU could post some data!

George

On 10/18/2017 10:35 AM, Marcia Boulina wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> George! George!
>
> 2017-10-18 10:16 GMT-04:00 Blair Rossetti <[hidden email]>:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> Post images on http://www.imgur.com and include the link in your posting.
>> *****
>>
>> Hi Friends,
>>
>> I am hoping to get access to some spectral microscopy data sets for
>> testing purposes. Ideally, I would like to aggregate a few spectral images
>> from different platforms and file formats. I've checked the Cell Image
>> Library and the repos listed on https://imagej.net/Public_data_sets , but
>> it seems that spectral data sets are scarce on the web. I would greatly
>> appreciate if someone could point me in the right direction.
>>
>> Thanks!
>> Blair
>>

--

George McNamara, PhD
Baltimore, MD 21231
[hidden email]
https://www.linkedin.com/in/georgemcnamara
https://works.bepress.com/gmcnamara/75 (may need to use Microsoft Edge or Firefox, rather than Google Chrome)
http://www.ncbi.nlm.nih.gov/myncbi/browse/collection/44962650
http://confocal.jhu.edu

July 2017 Current Protocols article, open access:
UNIT 4.4 Microscopy and Image Analysis
http://onlinelibrary.wiley.com/doi/10.1002/cphg.42/abstract
supporting materials direct link is
http://onlinelibrary.wiley.com/doi/10.1002/cphg.42/full#hg0404-sec-0023
figures at
http://onlinelibrary.wiley.com/doi/10.1002/cphg.42/figures

George McNamara

Re: Source for Spectral Image Data

In reply to this post by Blair Rossetti

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Hi Blair,

Spectral image files: I uploaded (#79) Leica SP8 confocal LIF (container
file of images) and (#80) Zeiss LSM510META (zip containing LSM files -
the short half of this META detector gets very few photons) spectral
images at

https://works.bepress.com/gmcnamara/79
https://works.bepress.com/gmcnamara/80

the individual images filenames summarize the acquisition settings, with
the metadata having more.

You should be able to make more Leica LIFs with images using the Leica
LAS X free download software in a "simulator" mode (I recommend
selecting a manual microscope to simulate).

I also manage a MetaMorph spectral imaging system (MetaMorph on Zeiss
microscope with PTI RatioMaster DeltaRAM random access monochromator),
http://confocal.jhu.edu/current-equipment/zeiss-upright-scope-w-pti-ratiomaster/
so if you need Meta 'spectral' image(s), please contact me directly.

Both #79 and #80 are from the same Leica Convallaria (Lily of the
Valley) microscope slide. Both Zeiss and Leica use this type of slide to
'prove' their instrument is working great.

Spectral data:

https://works.bepress.com/gmcnamara/9 for PubSpectra data (XLSX
inside) -- spectra were in UA Spectra Database
http://www.spectra.arizona.edu which needs Adobe Flash (maybe a good use
for a Windows XPwith I.E. 4.0).

More spectra data graphing sites are tabulated in
http://www.geomcnamara.com/light-microscopy-websites (draft of a CPHG
table).

http://www.photochemcad.com (keep an eye out for updates of this).

//

A major holiday is this Tuesday, 10/31, so I invite all confocal
listservees to play the Halloween Game - in addition to
self-identifying, you can try to find Martin Wessendorf, Jim Pawley, Guy
Cox, Claire Brown, Rosemary White, and Sylvie Le Guyader (if you cannot
see E.T. - the Extraterrestrial, in the top row, you may want to move on
to something else, like my recent CPHG Unit (url below).

https://www.linkedin.com/pulse/happy-halloween-george-mcnamara
https://www.linkedin.com/pulse/halloween-2016-trick-treat-can-you-self-identify-find-george-mcnamara

enjoy,

George
http://confocal.jhu.edu/gallery
http://www.geomcnamara.com/data

CPHG Unit is open access, lots of tables (with their own tab)
http://onlinelibrary.wiley.com/doi/10.1002/cphg.42/abstract

The Supporting Materials download link is in section
http://onlinelibrary.wiley.com/doi/10.1002/cphg.42/full#hg0404-sec-0023

On 10/18/2017 10:16 AM, Blair Rossetti wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi Friends,
>
> I am hoping to get access to some spectral microscopy data sets for testing purposes. Ideally, I would like to aggregate a few spectral images from different platforms and file formats. I've checked the Cell Image Library and the repos listed on https://imagej.net/Public_data_sets , but it seems that spectral data sets are scarce on the web. I would greatly appreciate if someone could point me in the right direction.
>
> Thanks!
> Blair