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Multi-Probe Microscopy

George McNamara, Ph.D.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Multi-Probe Microscopy 

Several web sites are used to increase file storage capacity of linked accounts. 

George McNamara, August 18, 2007 

http://home.earthlink.net/~mpmicro (Multi-Probe Microscopy doc; data tables Excel files)

http://home.earthlink.net/~fluorescentdyes (same web page as ~mpmicro)

http://home.earthlink.net/~geomcnamara

http://home.earthlink.net/~tiki_goddess  

Spectra Excel files  - See also the PubSpectra Web Site:

McNamara_Boswell_000_2006_Index_Dyes_FPs_Filters_Lamps_Other_Spectra.xls

McNamara_Boswell_Spectra_Dyes_FPs.zip

McNamara_Boswell_Spectra_Filters.zip

McNamara_Boswell_Spectra_Lamps_other.zip

http://home.earthlink.net/~fluorescentdyes/McNamara 20050709 FRET Janos Szollosi Horvath Gabor FRET calculator.xls        

 

PubSpectra is at http://home.earthlink.net/~pubspectra/

Fluorescent dye data table web addresses are below in the Fluorescent Dyes section. 

See also:

Carl Boswell / GM Fluorescent Spectra site http://www.mcb.arizona.edu/ipc/fret/default.htm (home page)

A manuscript about the U. Arizona Fluorescent Spectra (graphing) and PubSpectra (data download) websites was published:

McNamara G, Gupta A, Reynaert J, Coates TD, Boswell C: Spectral imaging microscopy web sites and data.

Cytometry. 69A: 863-871 (2006). PubMed Abstract. Link.

 

 

MPMicro download website

file version: May 2007

http://home.earthlink.net/~mpmicro/  

The current 2006 Multi-Probe Microscopy doc (mpmicro.doc) is in a zip file at

http://home.earthlink.net/~mpmicro/mpmicro.zip (7.0 Mb, May, 2007)

Fluorescent Proteins and Dyes Data Tables Downloads

file versions: August 2007

McNamara G, Boswell C (2007) A Thousand Proteins of Light: 

15 Years of Advances in Fluorescent Proteins.  

in Modern Research and Educational Topics in Microscopy (volume 3), in press.

http://www.formatex.org/microscopy3/    

 

Thousand proteins: Word doc (Draft)   Data  

McNamara 2007 Fluorophore Data Tables (>5000 dye entries, 3.2 Mb)

 

McNamara 2005 Objective Lens Tables (Leica, Nikon, Olympus, Zeiss biomedical microscope lenses).

(Microsoft 2000 Excel file - from June 2005).

These are also available from

http://home.earthlink.net/~pubspectra/

 

Bonus file:

In June 2005 the Journal of Histotechnology published an article by me on Color Balancing histology images. Dr. James Hendricks gave me permission to post the electronic PDF on my personal web site. This is an informal bit of "open access" publishing, since JoH does not have a clear policy on author's posting content. Thanks for permission Jim!

http://home.earthlink.net/~geomcnamara/McNamara2005JoH28n2pp81-88.pdf 

 

About these web sites:

I've been an Earthlink customer since moving to California in 1997. Currently (1/2006) and for the past few years, Earthlink has offered 80 Mb of "free personal web space" to its customers. Of course since I have to pay to be a customer, I don't think of this as free. A complication is that the 80 Mb are partitioned as 10 Mb for each of eight web sites. Since I am unwilling to spend more than necessary for Internet access/web space, and I had an unfavorable experience with a "free" site in 2004 that made a mess of my contribution to the 2004 PUCL Microscopy & Imaging CD. For the 2005 PUCL CD, I sent the spectral files to J. Paul Robinson's group to Purdue to be included directly on the CD (then I updated the Fluorescent Dyes Excel file to >5000 entries, and added a few more entries to the FPaa Excel file (web links above), putting the CD out of date before the MSA2005 conference where it is to be released).  

Ted Salmon says about MetaMorph, "I love MetaMorph, but it drives me crazy." (ok, I think he said "but", but maybe he said "because"). I have similar feelings about Earthlink. I suspect they are better than AOL ("the Internet on training wheels") but their tech support leaves a lot to be desired. On July 9, 2005, 3 hours were needed to solve a problem I was having connecting to the web space upload site(s). Fortunately not all of this was phone time (their e-chat support feature never did have someone type/chatting from their end). The solution turned out to be two-fold:

1) find the right department's support person to talk with. In my case: Oscar.

2) Oscar quickly keyed in to an option in WS_FTP (Connect dialog -> Advanced tab -> Enable Passive transfers) which is (in the words of the dialog) "necessary for some firewall and gateway configurations". 

Thanks Oscar!

Hindsight being 20/20, once this worked, I realized I had not been able to connect by FTP since installing a Firewall as a condition to use CoH's Internet access. I encourage Earthlink to spend a few minutes setting up an FAQ / help web page about connecting to their customer's personal web upload sites. 

 

 

 

 

 
George McNamara, Ph.D.

University of Miami

gmcnamara@med.miami.edu

Electronic Mail geomcnamara@earthlink.net  

Personal Web Page http://home.earthlink.net/~geomcnamara

I am also a consultant to the CHLA Congressman Julian Dixon Cellular Image Core, Childrens Hospital Los Angeles, directed by Professor Thomas D. Coates and managed by Dr. Yannan Ouyang.


June 2004 versions of MpMicro, Fluorescent Proteins Data, and Fluorophores Table, are on the
PUCL Cytometry Series CD-ROM "Microscopy 2", handed out at the August 2004 Microscopy Society of America (MSA) meeting by J. Paul Robinson, Purdue University Cytometry Lab (PUCL). The PUCL CD-ROM files are now way out of date. 

June 2005 versions are on the Purdue University Microscopy 3 CD-ROM, distributed at MSA 2005, Hawaii.

April 2006 versions of the files are on the PUCL Cytometry Series CD-ROM Cytometry CD9 / Microscopy CD4, distributed at the May 2006 ISAC meeting in Quebec City by J. Paul robinson of Purdue University.

Why am I posting the Excel files? Someday I intend to publish the fluorescent protein and Fluorophore Data Excel file data in a scientific journal. However, in the meantime, it might do some people some good to have it available online. If you use the data, please cite the original reference source. It would also be nice to cite me for collecting the data in one place. As for copyright - facts and data cannot be copyrighted, at least here in the USA (says so in the U.S. Constitution). Do I think the data has value? Yes, I do. Do I think I (or anyone else) should charge money for it? No, I don't. 

If you find the data of use, feel free to drop me a note. Even better, I welcome additional data, either from your own research, or that you've collected. Please email the data to me at geomcnamara@earthlink.net -- please use as your subject line something like: "Fluorophore data for George's Excel files and website" (you can leave out the quotation marks). The reason for a standard subject line is that I receive a lot of junk mail, and am especially leery of file attachments (both my office and home PC's have firewall and antivirus). If you send me data, please try to use the same format as the Excel file(s). When I start getting external contributions I will add an extra column in the Fluor data tables to acknowledge sources. You are also welcome to send me reprints (pdf's) of the data that you've tabulated and sent me. 

prism

The posted data files are really just the tip of the iceberg - or to pun on Carl Boswell and my Fluorescent Dye Spectra web site logo, Tip of the Prism. Someday we will post some or all of the spectra data that is on the site. See http://www.mcb.arizona.edu/ipc/fret/default.htm for the intro page to the Spectra site. 

December 9, 2004 xyztiλτθρηN$

I added a Microscopy Dimensions web page to this site, trying to count up the number of dimensions that can be imaged in one experiment (actually, one data acquisition run for one replicate of one experiment. 

Favorite Links

George McNamara personal web site

http://home.earthlink.net/~geomcnamara/ 

Cell Motion Analysis Temporal Area Map page 

Fluorescent Spectra Web Site (Carl Boswell & George McNamara - hosted by U. Arizona) 

Spectral traces for fluorescent dyes (Carl Boswell, U. Arizona) 

Pubmed (NIH, NLM, NCBI)

Pubmed with USC Helath Science Library e-Links

See pkzip or WinZip for programs that can unzip the mpmicro.zip. 

If you do not have Microsoft Word 2000 (or newer), you can download Microsoft Word Vierwer from the www.microsoft.com web site (newer versions of Microsoft Internet Explorer may enable viewing and saving of the Word doc). 

 

400 chromosome breast cancer metaphase spectral karyotype (SKY). Steve Goodison & George McNamara.

 

prism

 

 

Want to get in touch? You can send me e-mail at:

geomcnamara@earthlink.net 

Web sites updated August 18, 2007

 Copyright (c) 2004-2007 George McNamara