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index.html
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<!DOCTYPE html>
<!--[if IEMobile 7 ]><html class="no-js iem7"><![endif]-->
<!--[if lt IE 9]><html class="no-js lte-ie8"><![endif]-->
<!--[if (gt IE 8)|(gt IEMobile 7)|!(IEMobile)|!(IE)]><!--><html class="no-js" lang="en"><!--<![endif]-->
<head>
<meta charset="utf-8">
<title> - </title>
<meta name="author" content="Rich Stoner">
<meta name="description" content="The WholeSlide iPad app was developed to enable rapid access and rich interaction with large (1 gigapixel + ) wholeslide images hosted online. The …">
<!-- http://t.co/dKP3o1e -->
<meta name="HandheldFriendly" content="True">
<meta name="MobileOptimized" content="320">
<meta name="viewport" content="width=device-width, initial-scale=1">
<link rel="canonical" href="http://wholeslide.com">
<link href="/favicon.ico" rel="icon">
<link href="/stylesheets/screen.css" media="screen, projection" rel="stylesheet" type="text/css">
<script src="/javascripts/modernizr-2.0.js"></script>
<script src="/javascripts/ender.js"></script>
<script src="/javascripts/octopress.js" type="text/javascript"></script>
<link href="/atom.xml" rel="alternate" title="" type="application/atom+xml">
<!--Fonts from Google"s Web font directory at http://google.com/webfonts -->
<link href="http://fonts.googleapis.com/css?family=PT+Serif:regular,italic,bold,bolditalic" rel="stylesheet" type="text/css">
<link href="http://fonts.googleapis.com/css?family=PT+Sans:regular,italic,bold,bolditalic" rel="stylesheet" type="text/css">
<style type="text/css">
/**
* HTML5 ✰ Boilerplate
*
* style.css contains a reset, font normalization and some base styles.
*
* Credit is left where credit is due.
* Much inspiration was taken from these projects:
* - yui.yahooapis.com/2.8.1/build/base/base.css
* - camendesign.com/design/
* - praegnanz.de/weblog/htmlcssjs-kickstart
*/
/**
* html5doctor.com Reset Stylesheet (Eric Meyer's Reset Reloaded + HTML5 baseline)
* v1.6.1 2010-09-17 | Authors: Eric Meyer & Richard Clark
* html5doctor.com/html-5-reset-stylesheet/
*/
pre.ipynb {
color: black;
background: #f7f7f7;
border: 0;
box-shadow: none;
margin-bottom: 0;
padding: 0;}
h1.ipynb h2.ipynb h3.ipynb h4.ipynb h5.ipynb h6.ipynb {
h1.ipynb h2.ipynb ... {
margin: 0;
padding: 0;
border: 0;
font-size: 100%;
font: inherit;
vertical-align: baseline;
}
/*html, body,*/ div, span, object, iframe,
/*h1, h2, h3, h4, h5, h6,*/ p, blockquote, pre,
abbr, address, cite, code, del, dfn, em, img, ins, kbd, q, samp,
small, strong, sub, sup, var, b, i, dl, dt, dd, ol, ul, li,
fieldset, form, label, legend,
table, caption, tbody, tfoot, thead, tr, th, td,
article, aside, canvas, details, figcaption, figure,
footer, header, hgroup, menu, nav, section, summary,
time, mark, audio, video {
margin: 0;
padding: 0;
border: 0;
font-size: 100%;
font: inherit;
vertical-align: baseline;
}
sup { vertical-align: super; }
sub { vertical-align: sub; }
article, aside, details, figcaption, figure,
footer, header, hgroup, menu, nav, section {
display: block;
}
blockquote, q { quotes: none; }
blockquote:before, blockquote:after,
q:before, q:after { content: ""; content: none; }
ins { background-color: #ff9; color: #000; text-decoration: none; }
mark { background-color: #ff9; color: #000; font-style: italic; font-weight: bold; }
del { text-decoration: line-through; }
abbr[title], dfn[title] { border-bottom: 1px dotted; cursor: help; }
table { border-collapse: collapse; border-spacing: 0; }
hr { display: block; height: 1px; border: 0; border-top: 1px solid #ccc; margin: 1em 0; padding: 0; }
input, select { vertical-align: middle; }
/**
* Font normalization inspired by YUI Library's fonts.css: developer.yahoo.com/yui/
*/
div.ipynb { font:13px/1.231 sans-serif; *font-size:small; } /* Hack retained to preserve specificity */
select, input, textarea, button { font:99% sans-serif; }
/* Normalize monospace sizing:
en.wikipedia.org/wiki/MediaWiki_talk:Common.css/Archive_11#Teletype_style_fix_for_Chrome */
pre, code, kbd, samp { font-family: monospace, sans-serif; }
em,i { font-style: italic; }
b,strong { font-weight: bold; }
</style>
<style type="text/css">
/* Flexible box model classes */
/* Taken from Alex Russell http://infrequently.org/2009/08/css-3-progress/ */
.hbox {
display: -webkit-box;
-webkit-box-orient: horizontal;
-webkit-box-align: stretch;
display: -moz-box;
-moz-box-orient: horizontal;
-moz-box-align: stretch;
display: box;
box-orient: horizontal;
box-align: stretch;
}
.hbox > * {
-webkit-box-flex: 0;
-moz-box-flex: 0;
box-flex: 0;
}
.vbox {
display: -webkit-box;
-webkit-box-orient: vertical;
-webkit-box-align: stretch;
display: -moz-box;
-moz-box-orient: vertical;
-moz-box-align: stretch;
display: box;
box-orient: vertical;
box-align: stretch;
}
.vbox > * {
-webkit-box-flex: 0;
-moz-box-flex: 0;
box-flex: 0;
}
.reverse {
-webkit-box-direction: reverse;
-moz-box-direction: reverse;
box-direction: reverse;
}
.box-flex0 {
-webkit-box-flex: 0;
-moz-box-flex: 0;
box-flex: 0;
}
.box-flex1, .box-flex {
-webkit-box-flex: 1;
-moz-box-flex: 1;
box-flex: 1;
}
.box-flex2 {
-webkit-box-flex: 2;
-moz-box-flex: 2;
box-flex: 2;
}
.box-group1 {
-webkit-box-flex-group: 1;
-moz-box-flex-group: 1;
box-flex-group: 1;
}
.box-group2 {
-webkit-box-flex-group: 2;
-moz-box-flex-group: 2;
box-flex-group: 2;
}
.start {
-webkit-box-pack: start;
-moz-box-pack: start;
box-pack: start;
}
.end {
-webkit-box-pack: end;
-moz-box-pack: end;
box-pack: end;
}
.center {
-webkit-box-pack: center;
-moz-box-pack: center;
box-pack: center;
}
</style>
<style type="text/css">
/**
* Primary styles
*
* Author: IPython Development Team
*/
div.ipynb {
overflow: hidden;
}
span#save_widget {
padding: 5px;
margin: 0px 0px 0px 300px;
display:inline-block;
}
span#notebook_name {
height: 1em;
line-height: 1em;
padding: 3px;
border: none;
font-size: 146.5%;
}
.ui-menubar-item .ui-button .ui-button-text {
padding: 0.4em 1.0em;
font-size: 100%;
}
.ui-menu {
-moz-box-shadow: 0px 6px 10px -1px #adadad;
-webkit-box-shadow: 0px 6px 10px -1px #adadad;
box-shadow: 0px 6px 10px -1px #adadad;
}
.ui-menu .ui-menu-item a {
border: 1px solid transparent;
padding: 2px 1.6em;
}
.ui-menu .ui-menu-item a.ui-state-focus {
margin: 0;
}
.ui-menu hr {
margin: 0.3em 0;
}
#menubar_container {
position: relative;
}
#notification {
position: absolute;
right: 3px;
top: 3px;
height: 25px;
padding: 3px 6px;
z-index: 10;
}
#toolbar {
padding: 3px 15px;
}
#cell_type {
font-size: 85%;
}
div#main_app {
width: 100%;
position: relative;
}
span#quick_help_area {
position: static;
padding: 5px 0px;
margin: 0px 0px 0px 0px;
}
.help_string {
float: right;
width: 170px;
padding: 0px 5px;
text-align: left;
font-size: 85%;
}
.help_string_label {
float: right;
font-size: 85%;
}
div#notebook_panel {
margin: 0px 0px 0px 0px;
padding: 0px;
}
div#notebook {
overflow-y: scroll;
overflow-x: auto;
width: 100%;
/* This spaces the cell away from the edge of the notebook area */
padding: 5px 5px 15px 5px;
margin: 0px;
background-color: white;
}
div#pager_splitter {
height: 8px;
}
div#pager {
padding: 15px;
overflow: auto;
display: none;
}
div.ui-widget-content {
border: 1px solid #aaa;
outline: none;
}
.cell {
border: 1px solid transparent;
}
div.cell {
width: 100%;
padding: 5px 5px 5px 0px;
/* This acts as a spacer between cells, that is outside the border */
margin: 2px 0px 2px 0px;
}
div.code_cell {
background-color: white;
}
/* any special styling for code cells that are currently running goes here */
div.code_cell.running {
}
div.prompt {
/* This needs to be wide enough for 3 digit prompt numbers: In[100]: */
width: 11ex;
/* This 0.4em is tuned to match the padding on the CodeMirror editor. */
padding: 0.4em;
margin: 0px;
font-family: monospace;
text-align:right;
}
div.input {
page-break-inside: avoid;
}
/* input_area and input_prompt must match in top border and margin for alignment */
div.input_area {
color: black;
border: 1px solid #ddd;
border-radius: 3px;
background: #f7f7f7;
}
div.input_prompt {
color: navy;
border-top: 1px solid transparent;
}
div.output_wrapper {
/* This is a spacer between the input and output of each cell */
margin-top: 5px;
margin-left: 5px;
/* FF needs explicit width to stretch */
width: 100%;
/* this position must be relative to enable descendents to be absolute within it */
position: relative;
}
/* class for the output area when it should be height-limited */
div.output_scroll {
/* ideally, this would be max-height, but FF barfs all over that */
height: 24em;
/* FF needs this *and the wrapper* to specify full width, or it will shrinkwrap */
width: 100%;
overflow: auto;
border-radius: 3px;
box-shadow: inset 0 2px 8px rgba(0, 0, 0, .8);
}
/* output div while it is collapsed */
div.output_collapsed {
margin-right: 5px;
}
div.out_prompt_overlay {
height: 100%;
padding: 0px;
position: absolute;
border-radius: 3px;
}
div.out_prompt_overlay:hover {
/* use inner shadow to get border that is computed the same on WebKit/FF */
box-shadow: inset 0 0 1px #000;
background: rgba(240, 240, 240, 0.5);
}
div.output_prompt {
color: darkred;
/* 5px right shift to account for margin in parent container */
margin: 0 5px 0 -5px;
}
/* This class is the outer container of all output sections. */
div.output_area {
padding: 0px;
page-break-inside: avoid;
}
/* This class is for the output subarea inside the output_area and after
the prompt div. */
div.output_subarea {
padding: 0.4em 0.4em 0.4em 0.4em;
}
/* The rest of the output_* classes are for special styling of the different
output types */
/* all text output has this class: */
div.output_text {
text-align: left;
color: black;
font-family: monospace;
}
/* stdout/stderr are 'text' as well as 'stream', but pyout/pyerr are *not* streams */
div.output_stream {
padding-top: 0.0em;
padding-bottom: 0.0em;
}
div.output_stdout {
}
div.output_stderr {
background: #fdd; /* very light red background for stderr */
}
div.output_latex {
text-align: left;
color: black;
}
div.output_html {
}
div.output_png {
}
div.output_jpeg {
}
div.text_cell {
background-color: white;
padding: 5px 5px 5px 5px;
}
div.text_cell_input {
color: black;
border: 1px solid #ddd;
border-radius: 3px;
background: #f7f7f7;
}
div.text_cell_render {
font-family: "Helvetica Neue", Arial, Helvetica, Geneva, sans-serif;
outline: none;
resize: none;
width: inherit;
border-style: none;
padding: 5px;
color: black;
}
/* The following gets added to the <head> if it is detected that the user has a
* monospace font with inconsistent normal/bold/italic height. See
* notebookmain.js. Such fonts will have keywords vertically offset with
* respect to the rest of the text. The user should select a better font.
* See: https://github.com/ipython/ipython/issues/1503
*
* .CodeMirror span {
* vertical-align: bottom;
* }
*/
.CodeMirror {
line-height: 1.231; /* Changed from 1em to our global default */
}
.CodeMirror-scroll {
height: auto; /* Changed to auto to autogrow */
/* The CodeMirror docs are a bit fuzzy on if overflow-y should be hidden or visible.*/
/* We have found that if it is visible, vertical scrollbars appear with font size changes.*/
overflow-y: hidden;
overflow-x: auto; /* Changed from auto to remove scrollbar */
}
/* CSS font colors for translated ANSI colors. */
.ansiblack {color: black;}
.ansired {color: darkred;}
.ansigreen {color: darkgreen;}
.ansiyellow {color: brown;}
.ansiblue {color: darkblue;}
.ansipurple {color: darkviolet;}
.ansicyan {color: steelblue;}
.ansigrey {color: grey;}
.ansibold {font-weight: bold;}
.completions {
position: absolute;
z-index: 10;
overflow: hidden;
border: 1px solid grey;
}
.completions select {
background: white;
outline: none;
border: none;
padding: 0px;
margin: 0px;
overflow: auto;
font-family: monospace;
}
option.context {
background-color: #DEF7FF;
}
option.introspection {
background-color: #EBF4EB;
}
/*fixed part of the completion*/
.completions p b {
font-weight:bold;
}
.completions p {
background: #DDF;
/*outline: none;
padding: 0px;*/
border-bottom: black solid 1px;
padding: 1px;
font-family: monospace;
}
pre.dialog {
background-color: #f7f7f7;
border: 1px solid #ddd;
border-radius: 3px;
padding: 0.4em;
padding-left: 2em;
}
p.dialog {
padding : 0.2em;
}
.shortcut_key {
display: inline-block;
width: 15ex;
text-align: right;
font-family: monospace;
}
.shortcut_descr {
}
/* Word-wrap output correctly. This is the CSS3 spelling, though Firefox seems
to not honor it correctly. Webkit browsers (Chrome, rekonq, Safari) do.
*/
pre, code, kbd, samp { white-space: pre-wrap; }
#fonttest {
font-family: monospace;
}
.js-error {
color: darkred;
}
</style>
<style type="text/css">
.rendered_html {color: black;}
.rendered_html em {font-style: italic;}
.rendered_html strong {font-weight: bold;}
.rendered_html u {text-decoration: underline;}
.rendered_html :link { text-decoration: underline }
.rendered_html :visited { text-decoration: underline }
.rendered_html h1 {font-size: 197%; margin: .65em 0; font-weight: bold;}
.rendered_html h2 {font-size: 153.9%; margin: .75em 0; font-weight: bold;}
.rendered_html h3 {font-size: 123.1%; margin: .85em 0; font-weight: bold;}
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<p>The WholeSlide iPad app was developed to enable rapid access and rich interaction with large (1 gigapixel + ) wholeslide images hosted online. The app allows users to natively zoom into a wealth of image types: from neuroanatomy and developmental biology to pathology and histology resources. <a href="https://itunes.apple.com/us/app/wholeslide/id448006595?mt=8%E2%80%8E">It’s available free on the iTunes app store.</a></p>
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<center><small>Figure 1. Main Menu, Set Browser, and Tile Chooser. </small></center>
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<h3>Basic usage</h3>
<p>Select a site from the main menu to show a list of available data sets. Selecting a dataset will present the list of wholeslide images for that set available to view. Sites and sets are organized based on their own internal structure. Some sites are grouped by folder while others are searchable. Selecting an image will load it into the viewer.</p>
<h3>Controls</h3>
<p>The WholeSlide App provides tools to interact with wholeslide images on the iPad. Individual tools are toggled on and off using the buttons located immediately to the right of the Tile chooser. Tools can be dragged around the screen using their top handle. </p></p>
<h4>Image Metadata</h4>
<p>Here you will find pertinent slide data, including species, stain, native resolution, and attribution. We are limited by the information made available via each independent site and are working to increase the depth and breadth of this content.</p>
<h4>Image Adjustment</h4>
<p>Here you will find controls to adjust the bright, contrast, and RGB windows of the image. Thanks to the processing power of the iPad, we are able to perform these adjustments in real-time on the device itself. The RGB windows allow you to scale the relatively red, green, and blue channels, but the easiest way to understand how the RGB windows function is to try them yourself.</p>
<h4>Navigation</h4>
<p>Here you will find a thumbnail of the current image, the effective magnification in screen pixels, and a slider pad to quickly move between images within a dataset</p>
<h3>Adding/Remove data</h3>
<p>The WholeSlide application contains links to over 70 Terabytes of image data from the start. However, many researchers and clinicians have their data on University-run image servers. Users can add custom sites and data sets within the app itself. We currently support Zoomify-compatible single tiles and sites that provide an RSS feed of the available tiles.</p>
<ul>
<li><b><a href="http://brain-map.org">Allen Brain Atlas</a></b> - Comprehensive Mouse Brain Atlas</li>
<li><b><a href="http://brainmaps.org">UC Davis Brain Maps</a></b> - 60 Terabytes of wholeslide stacks from many organisms</li>
<li><b><a href="http://zebrafinch.org">CSHL Zebrafinch Atlas</a></b> - Nissl and Myelin stained orthogonal views</li>
<li><b><a href="http://images.aperio.com">Aperio SlideScanner Examples</a></b> - Expansive collection of high-quality wholeslide images</li>
<li><b><a href="http://wormatlas.org">WormAtlas Virtual Worm</a></b> - C. Elegans anatomic reference</li>
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