Jeremy D. Rogers - Postdoctoral Fellow, Northwestern University.

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<div class='header' macro='gradient vert [[ColorPalette::PrimaryLight]] [[ColorPalette::PrimaryMid]]'>
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<span class='siteTitle' refresh='content' tiddler='SiteTitle'></span>&nbsp;
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<div id='tiddlerDisplay'></div>
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<div class='toolbar' macro='toolbar [[ToolbarCommands::ViewToolbar]]'></div>
<div class='title' macro='view title'></div>
<div class='subtitle'><span macro='view modifier link'></span>, <span macro='view modified date'></span> (<span macro='message views.wikified.createdPrompt'></span> <span macro='view created date'></span>)</div>
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<div class='toolbar' macro='toolbar [[ToolbarCommands::EditToolbar]]'></div>
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<div class='editor' macro='edit text'></div>
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To get started with this blank [[TiddlyWiki]], you'll need to modify the following tiddlers:
* [[SiteTitle]] & [[SiteSubtitle]]: The title and subtitle of the site, as shown above (after saving, they will also appear in the browser title bar)
* [[MainMenu]]: The menu (usually on the left)
* [[DefaultTiddlers]]: Contains the names of the tiddlers that you want to appear when the TiddlyWiki is opened
You'll also need to enter your username for signing your edits: <<option txtUserName>>

These [[InterfaceOptions]] for customising [[TiddlyWiki]] are saved in your browser

Your username for signing your edits. Write it as a [[WikiWord]] (eg [[JoeBloggs]])

<<option txtUserName>>
<<option chkSaveBackups>> [[SaveBackups]]
<<option chkAutoSave>> [[AutoSave]]
<<option chkRegExpSearch>> [[RegExpSearch]]
<<option chkCaseSensitiveSearch>> [[CaseSensitiveSearch]]
<<option chkAnimate>> [[EnableAnimations]]

----
Also see [[AdvancedOptions]]

<<importTiddlers>>

Jeremy D. Rogers is a Postoctoral Fellow in Prof. [[Vadim Backman|http://www.bme.northwestern.edu/faculty_staff/core/backman.html]]'s [[Biophotonics Laboratory|http://biophotonics.bme.northwestern.edu]] at [[Northwestern University|http://northwestern.edu]].

!!!Contact:
Jeremy D. Rogers
BME, Tech E310
2145 Sheridan Rd.
Evanston, IL 60625
(847) 467-0393
jdrogers (at) northwestern.edu

!!!Education
2006 - ~PhD, Optical Sciences, University of Arizona
2003 - MS, Optical Sciences, University of Arizona
1999 - BS, Physics, Michigan Technological Univ.

!!!//Curriculum Vitae//
* [[CV|jdr-cv08.pdf]] in PDF format (last updated in 2008)
<<tiddler HideTiddlerTags>><<tiddler HideTiddlerSubtitle>><<tiddler HideTiddlerToolbar>>

Code, programs, tools, etc. written by J.D. Rogers

//All code on this page is Copyright J.D. Rogers. Please use, copy, modify and redistribute anything you find here, but please give credit where due. I prefer to keep a running list of authors in the top of the code, so add your name, write some code, and have fun.//
!!Programs
<<<
!!!~MCML_mpi
''MCML for parallel processing,'' for example on clusters or multiprocessor workstations.
[[MCML|http://labs.seas.wustl.edu/bme/Wang/mc.html]] is a multi-layered [[Monte Carlo|http://omlc.ogi.edu/software/mc]] simulation for studying light transport in random media. It was written by [[Steve Jacques|http://www.bme.ogi.edu/biomedicaloptics/jacques/]] and [[Lihong Wang|http://labs.seas.wustl.edu/bme/Wang/]] for light scattering in biological tissue (or other random media). This version is the minimal modification to the original that adds MPI support. Message Passing Interface (MPI) allows the code to be run in parallel across many processors (or cores) such as clusters, multi-processors workstations, etc. You will need a working installation of MPI such as [[open-mpi|http://www.open-mpi.org]].
* README
* tarball
* zip file
* Patch file

!!!nscat_MCML
''MCML modified to track and bin the number of scattering events'', and other parameters.
It also uses a more general 3-parameter phase function based on the ~Whittle-Matern correlation function. The phase function includes exponential, stretched-exponential, ~Henyey-Greenstein and mass-fractal type scattering functions.
<<<
!!Code snippets, matlab functions, etc
<<<
!!!Matlab functions
<<list filter [tag[matlab]]>>
<<<

<<tiddler HideTiddlerTags>>
<<tiddler HideTiddlerSubtitle>>
<<tiddler HideTiddlerToolbar>>

[[About]]

/%
|Name|HideTiddlerSubtitle|
|Source|http://www.TiddlyTools.com/#HideTiddlerSubtitle|
|Version|0.0.0|
|Author|Eric Shulman - ELS Design Studios|
|License|http://www.TiddlyTools.com/#LegalStatements <br>and [[Creative Commons Attribution-ShareAlike 2.5 License|http://creativecommons.org/licenses/by-sa/2.5/]]|
|~CoreVersion|2.1|
|Type|script|
|Requires|InlineJavascriptPlugin|
|Overrides||
|Description|hide a tiddler's subtitle (dates/created by) display|

Usage: <<tiddler HideTiddlerSubtitle>>

%/<script>
	var t=story.findContainingTiddler(place);
	if (!t || t.id=="tiddlerHideTiddlerSubtitle") return;
	var nodes=t.getElementsByTagName("*");
	for (var i=0; i<nodes.length; i++)
		if (hasClass(nodes[i],"subtitle"))
			nodes[i].style.display="none";
</script>

/%
|Name|HideTiddlerTags|
|Source|http://www.TiddlyTools.com/#HideTiddlerTags|
|Version|0.0.0|
|Author|Eric Shulman - ELS Design Studios|
|License|http://www.TiddlyTools.com/#LegalStatements <br>and [[Creative Commons Attribution-ShareAlike 2.5 License|http://creativecommons.org/licenses/by-sa/2.5/]]|
|~CoreVersion|2.1|
|Type|script|
|Requires|InlineJavascriptPlugin|
|Overrides||
|Description|hide a tiddler's tagged/tagging display elements|

Usage: <<tiddler HideTiddlerTags>>

%/<script>
	var t=story.findContainingTiddler(place);
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2009.02.26 [1.9.4] in $(), handle leading '#' on ID for compatibility with JQuery syntax
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2005.11.08 [1.0.0] initial release
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''Low-coherence Enhanced Backscattering''

LEBS is a coherence phenomenon resulting in a retroreflection of light from a random medium.

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jdrogers(at)northwestern.edu
(847) 467-0393
[img[JDR at Arthur's Seat, Edinburgh|jdr_arthursseat_cropped.jpg]]
Copyright © 2009
by J.D. Rogers

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!! Journal Papers
|17.|[[link|http://dx.doi.org/10.1016/j.pss.2009.06.014]]||''J.D. Rogers'', N.N. Perreault, T.D. Niederberger, C. Lichten, L.G. Whyte, J.L. Nadeau, "A life detection problem in a High Arctic microbial community," //Planetary and Space Science//, (In Press).|
|16.|[[link|http://www.opticsinfobase.org/abstract.cfm?uri=ol-34-17-2679]]|[[pdf|capoglu-OL-2009.pdf]] |İlker R. Çapoğlu, ''Jeremy D. Rogers'', Allen Taflove, and Vadim Backman, "Accuracy of the Born approximation in calculating the scattering coefficient of biological continuous random media," //Opt. Lett.// ''34'', 2679-2681 (2009).|
|15.|[[link|http://www.opticsinfobase.org/ol/abstract.cfm?URI=ol-34-12-1891]]|[[pdf|rogers-OL-2009.pdf]] |''Jeremy D. Rogers'', İlker R. Çapoğlu, and Vadim Backman, "Nonscalar elastic light scattering from continuous random media in the Born approximation," //Opt. Lett.// ''34'', 1891-1893 (2009).|
|14.|[[link|http://cancerres.aacrjournals.org/cgi/content/abstract/69/10/4476]]||Roy HK, Turzhitsky V, Kim Y, Goldberg MJ, Watson P, ''Rogers JD'', Gomes AJ, Kromine A, Brand RE, Jameel M, Bogovejic A, Pradhan P, Backman V., "Association between rectal optical signatures and colonic neoplasia: potential applications for screening," //Cancer Res.l// ''69''(10), 4476-83 (2009).|
|13.|[[link|http://clincancerres.aacrjournals.org/cgi/content/short/1078-0432.CCR-08-2880v1]]||Gomes AJ, Roy HK, Turzhitsky V, Kim Y, ''Rogers JD'', Ruderman S, Stoyneva V, Goldberg MJ, Bianchi LK, Yen E, Kromine A, Jameel M, Backman V., "Rectal mucosal microvascular blood supply increase is associated with colonic neoplasia," //Clin Cancer Res.// ''15''(9), 3110-7 (2009).|
|12.|[[link|http://www.opticsinfobase.org/ol/abstract.cfm?URI=ol-34-4-518]]||Hariharan Subramanian, Prabhakar Pradhan, Yang Liu, Ilker R. Capoglu, ''Jeremy D. Rogers'', Hemant K. Roy, Randall E. Brand, and Vadim Backman, "Partial-wave microscopic spectroscopy detects subwavelength refractive index fluctuations: an application to cancer diagnosis," //Opt. Lett.// ''34'', 518-520 (2009).|
|11.|[[link|http://www.pnas.org/content/105/51/20118.abstract]]||Hariharan Subramanian, Prabhakar Pradhan, Yang Liu, Ilker R. Capoglu, Xu Li, ''Jeremy D. Rogers'', Alexander Heifetz, Dhananjay Kunte, Hemant K. Roy, Allen Taflove, and Vadim Backman, "Optical methodology for detecting histologically unapparent nanoscale consequences of genetic alterations in biological cells." //PNAS//, 105:20118-20123 (2008).|
|10.|[[link|http://www.opticsinfobase.org/abstract.cfm?URI=ao-47-32-6046]]||Vladimir M. Turzhitsky, Andrew J. Gomes, Young L. Kim, Yang Liu, Alexey Kromine, ''Jeremy D. Rogers'', Mohammed Jameel, Hemant K. Roy, and Vadim Backman, "Measuring mucosal blood supply in vivo with a polarization-gating probe," Appl. Opt. ''47'', 6046-6057 (2008).|
|9.|[[link|http://www.gastrojournal.org/article/S0016-5085(08)01100-1/abstract]]||H. K. Roy, A. Gomes, V. Turzhitsky, M. J. Goldberg, ''J. Rogers'', S. Ruderman, Y. L. Kim, A. Kromine, R. E. Brand, M. Jameel, N. Hasabou, V. Backman, “Spectroscopic Microvascular Blood Detection from the Endoscopically Normal Colonic Mucosa: Biomarker for Neoplasia Risk”, Gastroenterology, 135(4), 1069-1078 (2008).|
|8.|[[link|http://dx.doi.org/10.1117/1.2978060]]|[[pdf|rogers_JBO_2008.pdf]] |''Jeremy D. Rogers'', Sara Landau, Tomasz S. Tkaczyk, Michael R. Descour, Mohammed S. Rahman, Rebecca ~Richards-Kortum, Ari H. O. Karkainen, and Todd Christenson, "Imaging performance of a miniature integrated microendoscope." //J. Biomed. Opt.// ''13'', 054020 (2008), DOI:10.1117/1.2978060|
|7.|[[link|http://www.opticsinfobase.org/ol/abstract.cfm?URI=ol-31-4-504]]|[[pdf|rogers-OL-2006.pdf]]|''J. D. Rogers'', T. S. Tkaczyk, M. R. Descour, A. H. O. Kärkkäinen, R. ~Richards-Kortum, “Removal of ghost images by using tilted element optical systems with polynomial surfaces for aberration compensation.” //Opt. Lett.// ''31'', 504-506 (2006).|
|6.|[[link|http://www.opticsinfobase.org/oe/abstract.cfm?URI=oe-12-16-3745]]|[[pdf|tkaczyk-OE-2004.pdf]] |T. S. Tkaczyk, M. Rahman, V. Mack, K. Sokolov, ''J. D. Rogers'', R. ~Richards-Kortum, and M. R. Descour, “High resolution, molecular-speciﬁc, reﬂectance imaging in optically dense tissue phantoms with structured-illumination.” //Optics Express//, (12), 3745-+, (2004).|
|5.|[[link|http://www.opticsinfobase.org/oe/abstract.cfm?URI=oe-12-7-1294]]|[[pdf|rogers-OE-2004.pdf]]|''J. D. Rogers'', A. H. O. Kärkkäinen, T. Tkaczyk, J. T. Rantala, M. Descour, “Realization of refractive microoptics through grayscale lithographic patterning of photosensitive hybrid glass.” //Optics Express//, (2004).|
|4.|[[link|http://www.opticsinfobase.org/oe/abstract.cfm?URI=oe-11-12-1436]]|[[pdf|lee-OE-2003.pdf]]|J. Lee, ''J. D. Rogers'', M. R. Descour, E. Hsu, J. S. Aaron, K. Sokolov, R. R. ~Richards-Kortum, “Imaging quality assessment of multi-modal miniature microscope.” //Optics Express//, (11) 1436-+ (2003).|
|3.|[[link|http://www.opticsinfobase.org/ao/abstract.cfm?URI=ao-41-19-3988]]||A. H. O. Karkkainen, J. M. Tamkin, ''J. D. Rogers'', D. R. Neal, O. E. Hormi, G. E. Jabbour, J. T. Rantala,  M. R. Descour, “Direct photolithographic deforming of organomodiﬁed siloxane ﬁlms for micro-optics fabrication.” //Applied Optics//, (41) 3988-3998 (2002).|
|2.|[[link|http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?tp=&arnumber=980264&isnumber=21116]]||M. R. Descour, A. H. O. Karkkainen, ''J. D. Rogers'', C. Liang, R. S. Weinstein, J. T. Rantala, B. Kilic, E.  Madenci, R. R. ~Richards-Kortum, E. V. Anslyn, R. D. Dupuis, R. J. Schul, C. G. Willison, C. P. Tigges, “Toward the development of miniaturized imaging systems for detection of pre-cancer.” //Quantum Electronics, IEEE Journal of//, (38):2 122-130 (2002).|
|1.|[[link|http://dx.doi.org/10.1119/1.1286048]]||R. Pastel, A. Struthers, R. Ringle, ''J. Rogers'', C. Rohde, P. Geiser, “Laser trapping of microscopic particles for undergraduate experiments.” //American Journal of Physics//, (68) 993-1001 (2000).|

!!Conference Presentations
#J. D. Rogers, H. Subramanian, V. Turzhitsky, V. Backman, "Relationship of Low-coherence Enhanced Backscattering Spectroscopy measurements to optical properties of scattering media." BIOS, SPIE Photonics West, January, 2009. ''(Invited)''
#J. D. Rogers, H. Subramanian, V. Turzhitsky, P. Pradhan, Y. L. Kim, A. Taﬂove, and V. Backman, "Enhanced Backscattering for Tissue Characterization and Diagnosis." ~AP-/URSI, San Diego, 2008. ''(Invited)''
#Jeremy&nbsp;D.&nbsp;Rogers,&nbsp;Vladimir&nbsp;M.&nbsp;Turzhitsky,&nbsp;Nikhil&nbsp;N.&nbsp;Mutyal,&nbsp;Andrew&nbsp;Gomes,&nbsp;Alexey&nbsp;Kromin,&nbsp;Vadim&nbsp;Backman, "An Endoscope Compatible Low‐Coherence Enhanced Backscattering Spectroscopy Probe for Cancer Screening." Poster ~BTuF10, OSA ~BioMed Topical Meeting, March, 2008.
# J. D. Rogers, T. S. Tkaczyk, M. S. Rahman, R. R. ~Richards-Kortum, T. C. Christenson, M. R. Descour, “Integrated miniature microscope with structured illumination for in vivo microscopy.” Optical Diagnostic Imaging from Bench to Bedside at the National Institutes of Health, (2006).
#J. D. Rogers, T. S. Tkazcyk, M. R. Descour, A. H. O. Kärkkäinen, M. S. Rahman and R. ~Richards-Kortum, “Imaging with a miniature microscope constructed from grayscale lithographically patterned refractive microlenses.” OSA Topical Meeting on Diffractive Optics and Micro Optics (2004).
# J. D. Rogers, J. Lee, A. H. O. Kärkkäinen, T. Tkaczyk, M. R. Descour, “Gray-scale lithographic fabrication of optomechanical features using hybrid sol-gel glass for precision assembly of miniature imaging systems.” SPIE Annual Meeting: Gradient Index, Miniature, and Diffractive Optical Systems III. Proceedings of SPIE 5177 (2003).
# J. D. Rogers, T. Tkazcyk, M. R. Descour, T. R. Christenson, “Characterization and testing of a MEMS scanning grating for structured illumination in a miniature microscope.” FIO and Laser Science, OSA Anual Meeting, Oct. 5-9, 2003.
# J. D. Rogers, C. Liang, A. H. Kärkkäinen, M. R. Descour, “Fabrication and assembly of microoptical imaging systems.” Photonics West, SPIE, (2002).
#J. D. Rogers, M. R. Descour, A. H. O. Kärkkäinen, R. J. Shul, C. G. Willison, C. P. Tigges, “Fabrication and assembly of miniature imaging systems using lithographically patterned microoptics and silicon microstructures.” OSA Topical Meeting on Diffractive Optics and Micro Optics (2002).
#J. D. Rogers, C. Ftaclas, “Coronagraphs for Small Telescopes.” American Astronomical Society Meeting Abstracts, 194 (1999).

!!Patents

!!Book Chapters
*//Biomedical Applications of Light Scattering//, Chapter 2, "Light Scattering from Continuous Random Media," İlker R. Çapoğlu, Jeremy D. Rogers, and Vadim Backman, ed. A. Wax, V. Backman, ~McGraw Hill, (2009).
*//Biomedical Applications of Light Scattering//, Chapter 14, "Enhanced Backscattering and """Low-Coherence""" Enhanced Backscattering Spectroscopy," J. D. Rogers, Vladimir Turzhitsky, Young. Kim, Vadim Backman, ed. A. Wax, V. Backman, ~McGraw Hill, (2009).

!!Dissertation
[[PDF|jdrdiss2006.pdf]] //Miniature microscope design and construction based on tilted rotationally asymmetric printed lenses//, University of Arizona, 2006.

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Projects and areas of interest

!!Theory
*Light scattering from continuously random media
* Relationship between optical properties and refractive index model parameters

!!Simulation
* Monte Carlo modeling of light transport in random/turbid media
* Numerical simulation of [[LEBS]]

!!Experiment
* experimental [[LEBS]]  
* Spectral microscopy
* Optical metrology

!!Design and engineering
* Design of fiber optic probes for //in vivo// clinical trials
* Optical design for imaging and non-imaging detection of scattered light

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2008.10.17 [2.9.6] changed chkSinglePageAutoScroll default to false
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	config.options.chkSinglePageKeepEditedTiddlers=false;
if (config.options.chkTopOfPageMode==undefined)
	config.options.chkTopOfPageMode=false;
if (config.options.chkBottomOfPageMode==undefined)
	config.options.chkBottomOfPageMode=false;
if (config.options.chkSinglePageAutoScroll==undefined)
	config.options.chkSinglePageAutoScroll=false;
//}}}
//{{{
config.SPMTimer = 0;
config.lastURL = window.location.hash;
function checkLastURL()
{
	if (!config.options.chkSinglePageMode)
		{ window.clearInterval(config.SPMTimer); config.SPMTimer=0; return; }
	if (config.lastURL == window.location.hash) return; // no change in hash
	var tids=decodeURIComponent(window.location.hash.substr(1)).readBracketedList();
	if (tids.length==1) // permalink (single tiddler in URL)
		story.displayTiddler(null,tids[0]);
	else { // restore permaview or default view
		config.lastURL = window.location.hash;
		if (!tids.length) tids=store.getTiddlerText("DefaultTiddlers").readBracketedList();
		story.closeAllTiddlers();
		story.displayTiddlers(null,tids);
	}
}


if (Story.prototype.SPM_coreDisplayTiddler==undefined)
	Story.prototype.SPM_coreDisplayTiddler=Story.prototype.displayTiddler;
Story.prototype.displayTiddler = function(srcElement,tiddler,template,animate,slowly)
{
	var title=(tiddler instanceof Tiddler)?tiddler.title:tiddler;
	var tiddlerElem=document.getElementById(story.idPrefix+title); // ==null unless tiddler is already displayed
	var opt=config.options;
	var single=opt.chkSinglePageMode && !startingUp;
	var top=opt.chkTopOfPageMode && !startingUp;
	var bottom=opt.chkBottomOfPageMode && !startingUp;
	if (single) {
		story.forEachTiddler(function(tid,elem) {
			// skip current tiddler and, optionally, tiddlers that are folded.
			if (	tid==title
				|| (opt.chkSinglePageKeepFoldedTiddlers && elem.getAttribute("folded")=="true"))
				return;
			// if a tiddler is being edited, ask before closing
			if (elem.getAttribute("dirty")=="true") {
				if (opt.chkSinglePageKeepEditedTiddlers) return;
				// if tiddler to be displayed is already shown, then leave active tiddler editor as is
				// (occurs when switching between view and edit modes)
				if (tiddlerElem) return;
				// otherwise, ask for permission
				var msg="'"+tid+"' is currently being edited.\n\n";
				msg+="Press OK to save and close this tiddler\nor press Cancel to leave it opened";
				if (!confirm(msg)) return; else story.saveTiddler(tid);
			}
			story.closeTiddler(tid);
		});
	}
	else if (top)
		arguments[0]=null;
	else if (bottom)
		arguments[0]="bottom";
	if (single && opt.chkSinglePagePermalink && !config.browser.isSafari) {
		window.location.hash = encodeURIComponent(String.encodeTiddlyLink(title));
		config.lastURL = window.location.hash;
		document.title = wikifyPlain("SiteTitle") + " - " + title;
		if (!config.SPMTimer) config.SPMTimer=window.setInterval(function() {checkLastURL();},1000);
	}
	if (tiddlerElem && tiddlerElem.getAttribute("dirty")=="true") { // editing... move tiddler without re-rendering
		var isTopTiddler=(tiddlerElem.previousSibling==null);
		if (!isTopTiddler && (single || top))
			tiddlerElem.parentNode.insertBefore(tiddlerElem,tiddlerElem.parentNode.firstChild);
		else if (bottom)
			tiddlerElem.parentNode.insertBefore(tiddlerElem,null);
		else this.SPM_coreDisplayTiddler.apply(this,arguments); // let CORE render tiddler
	} else
		this.SPM_coreDisplayTiddler.apply(this,arguments); // let CORE render tiddler
	var tiddlerElem=document.getElementById(story.idPrefix+title);
	if (tiddlerElem&&opt.chkSinglePageAutoScroll) {
		// scroll to top of page or top of tiddler
		var isTopTiddler=(tiddlerElem.previousSibling==null);
		var yPos=isTopTiddler?0:ensureVisible(tiddlerElem);
		// if animating, defer scroll until after animation completes
		var delay=opt.chkAnimate?config.animDuration+10:0;
		setTimeout("window.scrollTo(0,"+yPos+")",delay); 
	}
}

if (Story.prototype.SPM_coreDisplayTiddlers==undefined)
	Story.prototype.SPM_coreDisplayTiddlers=Story.prototype.displayTiddlers;
Story.prototype.displayTiddlers = function() {
	// suspend single/top/bottom modes when showing multiple tiddlers
	var opt=config.options;
	var saveSPM=opt.chkSinglePageMode; opt.chkSinglePageMode=false;
	var saveTPM=opt.chkTopOfPageMode; opt.chkTopOfPageMode=false;
	var saveBPM=opt.chkBottomOfPageMode; opt.chkBottomOfPageMode=false;
	this.SPM_coreDisplayTiddlers.apply(this,arguments);
	opt.chkBottomOfPageMode=saveBPM;
	opt.chkTopOfPageMode=saveTPM;
	opt.chkSinglePageMode=saveSPM;
}
//}}}

Postdoctoral Fellow, Northwestern University<<tiddler ToggleRightSidebar with: ".">>

Jeremy D. Rogers

/*{{{*/
/*Mocha TiddlyWiki Theme*/
/*Version 1.0*/
/*Design and CSS originally by Anthonyy, ported to TiddlyWiki by Saq Imtiaz.*/
/*}}}*/
/*{{{*/
 #contentWrapper{
margin: 0 3.4em;

			font-family: Lucida Grande, Tahoma, Arial, Helvetica, sans-serif; /* Lucida Grande for the Macs, Tahoma for the PCs */
font-size: 11px;
			line-height: 1.6em;
			color: #666;
}

.header {
 background: #fff; 
			padding-top: 10px;
			clear: both;

border-bottom: 4px solid #948979;
}

.headerShadow {	padding: 2.6em 0em 0.5em 0em; }

.siteTitle {
			font-family: 'Trebuchet MS' sans-serif;
			font-weight: bold;
			font-size: 32px;
			color: #CC6633;
			margin-bottom: 30px;
			background-color: #FFF;
}

.siteTitle a{color:#CC6633; border-bottom:1px dotted #cc6633;}

.siteSubtitle {
	font-size: 1.0em;
        display: block;
        margin: .5em 3em; color: #999999;
}

#mainMenu {
position:relative;
float:left;
margin-bottom:1em;
display:inline;
text-align:left;
padding: 2em 0.5em 0.5em 0em;
width:13em;
font-size:1em;
}

#sidebar{
position:relative;
float:right;
margin-bottom:1em;
padding-top:2em;
display:inline;

}

#displayArea {
	margin: 0em 17em 0em 15em;
}

.tagClear {clear:none;}

#contentFooter {background:#575352; color:#BFB6B3; clear: both; padding: 0.5em 1em;}

		
		#contentFooter a {
			color: #BFB6B3;
			border-bottom: 1px dotted #BFB6B3;
		}
		
		#contentFooter a:hover {
			color: #FFFFFF;
			background-color:#575352;
		}

		a,#sidebarOptions .sliderPanel a{
			color:#CC6714;
			text-decoration: none;
		}

		a:hover,#sidebarOptions .sliderPanel a:hover {
			color:#CC6714;
			background-color: #F5F5F5; 
		}

.viewer .button, .editorFooter .button{
	color: #666;
	border: 1px solid #CC6714;
}

.viewer .button:hover, 
.editorFooter .button:hover{
	color: #fff;
	background: #CC6714;
	border-color: #CC6714;
}

.viewer .button:active, .viewer .highlight,.editorFooter .button:active, .editorFooter .highlight{color:#fff; background:#575352;border-color:#575352;}


		#mainMenu a {
			display: block;
			padding: 5px;
			border-bottom: 1px solid #CCC;
		}

		#mainMenu a:link, #navlist a:visited {
			color:#CC6714;
			text-decoration: none;
		}
		
		#mainMenu a:hover {
			background: #000000 url(arrow.gif) 96% 50% no-repeat;
			background-color: #F5F5F5;
			color:#CC6714;
		}
		
		#mainMenu a:hover, #mainMenu a:active, #mainMenu .highlight, #mainMenu .marked {
			background: #000000 url(arrow.gif) 96% 50% no-repeat;
			background-color: #F5F5F5;
			color:#CC6714;
		}

#mainMenu span {position:relative;}

#mainMenu br {display:none;}

#sidebarOptions a {
			color:#999;
			text-decoration: none;
		}

#sidebarOptions	a:hover {
			color:#4F4B45;
			background-color: #F5F5F5;border:1px solid #fff;
		}

#sidebarOptions {line-height:1.4em;}

		.tiddler {
			padding-bottom: 40px;
			border-bottom: 1px solid #DDDDDD; 
		}
.title {color:#CC6633;}
.subtitle, .subtitle a { color: #999999; font-size: 1.0em;margin:0.2em;}
.shadow .title{color:#948979;}

.selected .toolbar a {color:#999999;}
.selected .toolbar a:hover {color:#4F4B45; background:transparent;border:1px solid #fff;}

.toolbar .button:hover, .toolbar .highlight, .toolbar .marked, .toolbar a.button:active{color:#4F4B45; background:transparent;border:1px solid #fff;}

 .listLink,#sidebarTabs .tabContents {line-height:1.5em;}
 .listTitle {color:#888;}

#sidebarTabs .tabContents {background:#fff;}
#sidebarTabs .tabContents .tiddlyLink, #sidebarTabs .tabContents .button{color:#999;}
#sidebarTabs .tabContents .tiddlyLink:hover,#sidebarTabs .tabContents .button:hover{color:#4F4B45;background:#fff}

#sidebarTabs .tabContents .button:hover, #sidebarTabs .tabContents .highlight, #sidebarTabs .tabContents .marked, #sidebarTabs .tabContents a.button:active{color:#4F4B45;background:#fff}

.tabSelected{color:#fff; background:#948979;}

.tabUnselected {
 background: #ccc;
}

 .tabSelected, .tabSelected:hover {
 color: #fff;
 background: #948979;
 border: solid 1px #948979;
padding-bottom:1px;
}

 .tabUnselected {
 color: #999;
 background: #eee;
 border: solid 1px #ccc;
padding-bottom:1px;
}

#sidebarTabs .tabUnselected { border-bottom: none;padding-bottom:3px;}
#sidebarTabs .tabSelected{padding-bottom:3px;}


#sidebarTabs .tabUnselected:hover { border-bottom: none;padding-bottom:3px;color:#4F4B45}

#sidebarOptions .sliderPanel {
	background: #fff; border:none;
	font-size: .9em;
}
#sidebarOptions .sliderPanel a {font-weight:normal;}
#sidebarOptions .sliderPanel input {border:1px solid #999;}

.viewer blockquote {
	border-left: 3px solid #948979;
}

.viewer table {
	border: 2px solid [[ColorPalette::TertiaryDark]];
}

.viewer th, thead td {
	background: #948979;
	border: 1px solid #948979;
	color: #fff;
}
.viewer pre {
	border: 1px solid #948979;
	background: #f5f5f5;
}

.viewer code {
	color: #2F2A29;
}

.viewer hr {
	border-top: dashed 1px #948979;
}

.editor input {
	border: 1px solid #948979;
}

.editor textarea {
	border: 1px solid #948979;
}

.popup {
	background: #948979;
	border: 1px solid #948979;
}

.popup li.disabled {
	color: #000;
}

.popup li a, .popup li a:visited {
	color: #eee;
	border: none;
}

.popup li a:hover {
	background: #575352;
	color: #fff;
	border: none;
}

.tagging, .tagged {
	border: 1px solid #eee;
	background-color: #F7F7F7;
}

.selected .tagging, .selected .tagged {
	background-color: #eee;
	border: 1px solid #BFBAB3;
}

 .tagging .listTitle, .tagged .listTitle {
	color: #bbb;
}

.selected .tagging .listTitle, .selected .tagged .listTitle {
	color: #666; 
}

.tagging .button, .tagged .button {
		color:#aaa;
}
.selected .tagging .button, .selected .tagged .button {
		color:#4F4B45;
}

.highlight, .marked {background:transparent; color:#111; border:none; text-decoration:underline;}

.tagging .button:hover, .tagged .button:hover, .tagging .button:active, .tagged .button:active {
		border: none; background:transparent; text-decoration:underline; color:#000;
}

h1,h2,h3,h4,h5 { color: #666; background: transparent; padding-bottom:2px; font-family: Arial, Helvetica, sans-serif; }
h1 {font-size:18px;}
h2 {font-size:16px;}
h3 {font-size: 14px;}

#messageArea {
	border: 4px solid #948979;
	background: #f5f5f5;
	color: #999;
        font-size:90%;
}

#messageArea a:hover { background:#f5f5f5;}

#messageArea .button{
	color: #666;
	border: 1px solid #CC6714;
}

#messageArea .button:hover {
	color: #fff;
	background: #948979;
	border-color: #948979;
}


* html .viewer pre {
	margin-left: 0em;
}

* html .editor textarea, * html .editor input {
	width: 98%;
}

.searchBar {float:right;font-size: 1.0em;}
.searchBar .button {color:#999;display:block;}
.searchBar .button:hover {border:1px solid #fff;color:#4F4B45;}
.searchBar input {			
                        background-color: #FFF;
			color: #999999;
			border: 1px solid #CCC;		margin-right:3px;
}

#sidebarOptions .button:active, #sidebarOptions .highlight {background:#F5F5F5;}

*html #contentFooter { padding:0.25em 1em 0.5em 1em;}

#noticeBoard {font-size: 0.9em; color:#999; position:relative;display:block;background:#fff; clear: both; margin-right:0.5em; margin-top:60px; padding:5px; border-bottom: 1px dotted #CCC; border-top: 1px dotted #CCC;}
#mainMenu #noticeBoard a,#mainMenu #noticeBoard .tiddlyLink {display:inline;border:none;padding:5px 2px;color:#DF9153 }
#noticeBoard a:hover {border:none;}	

#noticeBoard br {display:inline;}

#mainMenu #noticeBoard  .button{
	color: #666;
	border: 1px solid #DF9153;padding:2px;
}

#mainMenu #noticeBoard  .button:hover{
	color: #fff;
	background: #DF9153;
	border-color: #DF9153;
}

.searchbar {position:relative; width:11em;}
.searchbar .button{margin:0; width:11em;}
#header {display:block;}  /%#header {display:inline-block;}    %/ /%commented out to fix firefox 3.5.2 -- jDR %/ 
/*}}}*/

/%
|Name|ToggleRightSidebar|
|Source|http://www.TiddlyTools.com/#ToggleRightSidebar|
|Version|2.0.0|
|Author|Eric Shulman - ELS Design Studios|
|License|http://www.TiddlyTools.com/#LegalStatements <br>and [[Creative Commons Attribution-ShareAlike 2.5 License|http://creativecommons.org/licenses/by-sa/2.5/]]|
|~CoreVersion|2.1|
|Type|script|
|Requires|InlineJavascriptPlugin|
|Overrides||
|Description|show/hide right sidebar (MainMenu)|

Usage: <<tiddler ToggleRightSidebar with: "label">>

Config settings:
	config.options.chkShowRightSidebar (true)
	config.options.txtToggleRightSideBarLabelShow (◄)
	config.options.txtToggleRightSideBarLabelHide (►)

%/<script label="$1" title="show/hide right sidebar content">
	var co=config.options;
	if (co.chkShowRightSidebar=='undefined') co.chkShowRightSidebar=true;
	co.chkShowRightSidebar=!co.chkShowRightSidebar;
	var sb=document.getElementById('sidebar'); if (!sb) return;
	sb.style.display=co.chkShowRightSidebar?'block':'none';
	document.getElementById('displayArea').style.marginRight=co.chkShowRightSidebar?'':'1em';
	saveOptionCookie('chkShowRightSidebar');
	var labelShow=co.txtToggleRightSideBarLabelShow||'&#x25C4;';
	var labelHide=co.txtToggleRightSideBarLabelHide||'&#x25BA;';
	if (typeof(place)!='undefined' && '$1'=='$'+'1') {
		place.innerHTML=co.chkShowRightSidebar?labelHide:labelShow;
		place.title=(co.chkShowRightSidebar?'hide':'show')+' right sidebar';
	}
	var sm=document.getElementById('storyMenu'); if (sm) config.refreshers.content(sm);
</script><script>
	var co=config.options;
	if (co.chkShowRightSidebar=='undefined') co.chkShowRightSidebar=true;
	var sb=document.getElementById('sidebar'); if (!sb) return;
	sb.style.display=co.chkShowRightSidebar?'block':'none';
	document.getElementById('displayArea').style.marginRight=co.chkShowRightSidebar?'':'1em';
	if ('$1'=='$'+'1') {
		var labelShow=co.txtToggleRightSideBarLabelShow||'&#x25C4;';
		var labelHide=co.txtToggleRightSideBarLabelHide||'&#x25BA;';
		place.lastChild.innerHTML=co.chkShowRightSidebar?labelHide:labelShow;
		place.lastChild.title=(co.chkShowRightSidebar?'hide':'show')+' right sidebar';
	}
</script>

<!--{{{-->
<div class='toolbar' macro='toolbar [[ToolbarCommands::ViewToolbar]]'></div>
<div class='title' macro='view title'></div>
<div class='subtitle'><span macro='view modifier link'></span>, <span macro='view modified date'></span> (<span macro='message views.wikified.createdPrompt'></span> <span macro='view created date'></span>)</div>
<div class='tagging' macro='tagging'></div>
<div class='tagged' macro='tags'></div>
<div class='viewer' macro='view text wikified'></div>
<div class='tagClear'></div>
<span macro="tiddler ReplaceDoubleClick with: shift doubleclick"></span>
<!--}}}-->

This webpage is a single file called a [[TiddlyWiki|http://www.tiddlywiki.com]] © Osmosoft version <<version>>

{{{
% Find the center of the peak of a 2D peaked array
% There are two forms of this function depending on the number of
% arguments used to call it:
% (1) if called with 2 args, first smooth by convolution to make this 
% routine insensative to noise, then find the max of the smoothed array 
% (2) if called with 4 args, a faster averaging method is used, where the 
% rows are summed to find the peak in x, then the cols are summed to find
% the peak in y. The only problem with this method is that if there is an 
% inverse peak (dip) that lines up in x or y with the peak, they will
% cancel and the peak will not be located. To account for this, the extra
% args are the approximate position of the peak and the array is only
% summed over the smoothsize width around the peak position.
%
% written by Jeremy D. Rogers on June 30, 2009 (20090630)
% last updated: 20090916 by: jdrogers
%
% Notes: 

function center = findpeak(a, smoothsize, r,c)
if (nargin == 2)
   % convolution with a box is an effective smoothing method
   %a=convn(a,ones(smoothsize)/smoothsize,'same');
   
   %n = [4*smoothsize 4*smoothsize];
   %sigma = smoothsize;
   %h = fspecial('gaussian',n,sigma);
   a=filter2(ones(smoothsize),a);
   
   [y,x]=find(a==max(max(a)));
end
if (nargin == 4)
   sm=round(smoothsize/2);
   y=find(sum(a((c-sm):(c+sm),(r-sm):(r+sm)),2)==max(sum(a((c-sm):(c+sm),(r-sm):(r+sm)),2)))+(c-sm);
   x=find(sum(a((c-sm):(c+sm),(r-sm):(r+sm)),1)==max(sum(a((c-sm):(c+sm),(r-sm):(r+sm)),1)))+(r-sm);
end
center = [x,y];

}}}

//{{{
//This ensures that the footer sticks to the bottom of the screen when there are no tiddlers open. If that is not desirable, it can be deleted.
function setFooter() {
         if (document.getElementById && document.getElementById("contentFooter") ) {
            var windowHeight=findWindowHeight();
         if (windowHeight>0) {
            var contentHeight= document.getElementById('mainMenu').offsetHeight + document.getElementById("header").offsetHeight + document.getElementById("contentFooter").offsetHeight;
            var menu= document.getElementById('mainMenu');
            if (windowHeight-(contentHeight)>=0) {
               menu.style.position='relative';
               menu.style.marginBottom=(windowHeight-(contentHeight))+'px';
               }
            else {
                 menu.style.position='';
                 menu.style.marginBottom='';
                 }
            }
         }
}
window.onresize = function() {
  setFooter();
}

Story.prototype.refreshTiddler_footerhack=Story.prototype.refreshTiddler;
Story.prototype.refreshTiddler = function (title,template,force)
{    
var theTiddler = Story.prototype.refreshTiddler_footerhack.apply(this,arguments);
setFooter();
   return theTiddler;}

//}}}

{{{
% function to find a rotational average around a center point from a 2D arr
% rotational averaging about center (c1,c2) with sub array of length (len)
%
% written by Jeremy D. Rogers on June 30, 2009 (20090630)
% last updated: 20090630 by: jdrogers
%
% Notes: may want to try to further vectorize this to avoid the for loop 

function ravg = rotavg(a2, len, c1, c2)
a2sub = a2((c2-len):(c2+len),(c1-len):(c1+len));

dist = ((-len:len)'*(ones(1,2*len+1))).^2;dist = (dist+dist').^.5;
dist = round(dist)+1; % round to nearest pixel and add 1 (start index)

% masking corners should not be necessary
%mask=dist;mask(dist<len)=1;mask(dist>=len)=0; % create mask for zeroing corners
%dist(dist>N)=N; % keep index values from exceeding 1D matrix dimension

ravg = 1:len+1;
for i=1:len+1
    ravg(i)=mean(a2sub(dist==i));
end
}}}

//{{{
config.options.chkSinglePageMode = true;
config.options.chkSinglePagePermalink = true;
config.options.chkShowRightSidebar = false;
//}}}