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Metadata.html
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<!doctype html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no">
<title>Image Analysis with Fiji</title>
<link rel="stylesheet" href="css/reveal.css">
<link rel="stylesheet" href="css/theme/cci.css">
<link href="https://fonts.googleapis.com/css?family=Poppins" rel="stylesheet">
<!-- Theme used for syntax highlighting of code -->
<link rel="stylesheet" href="lib/css/zenburn.css">
<!-- Printing and PDF exports -->
<script>
var link = document.createElement( 'link' );
link.rel = 'stylesheet';
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document.getElementsByTagName( 'head' )[0].appendChild( link );
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<body>
<div class="reveal">
<!-- Header logo -->
<!--img style="position:fixed;top:1em;right:1em;" src="img/logo_cci.png" width="15%"-->
<!-- Slide Title -->
<header style="position: absolute;top: 1em; left: 1em; z-index:10;"></header>
<!-- ---------------------- START OF SLIDES -------------------------- -->
<div class="slides">
<section data-menu-title="Title">
<h2>Metadata</h2>
<h4>Erick Martins Ratamero<br>Research Fellow</h4>
</section>
<!--First subsession - What is metadata; essential metadata and what difference it makes --->
<section data-menu-title="Metadata" data-state="fiji6"><style>.fiji6 header:after { content: "What is metadata?"; }</style>
<p>Associated with the image, rather than part of the image itself. "Data about the data". Can encode anything from time of capture to specific microscope parameters that were being used.</p>
</section>
<section data-state="fiji6"><style>.fiji6 header:after { content: "What is metadata?"; }</style>
<p>Most essential one: dimensions (pixel size, Z separation, timepoints, channels)</p>
</section>
<section data-state="fiji6"><style>.fiji6 header:after { content: "What is metadata?"; }</style>
<p>But why? well, you don't want your measurements to be messed up</p>
</section>
<!--Second subsession - Looking at metadata in Fiji; setting calibrations, scale bars --->
<section data-state="fiji7"><style>.fiji7 header:after { content: "Metadata in Fiji"; }</style>
<p>Image -> Properties</p>
</section>
<section data-state="fiji7"><style>.fiji7 header:after { content: "Metadata in Fiji"; }</style>
<p>Check your channels</p>
</section>
<section data-state="fiji7"><style>.fiji7 header:after { content: "Metadata in Fiji"; }</style>
<p>Scale bars and how they can be wrong (quick comment on overlays)</p>
</section>
<!--Third subsession - Bioformats and how to open/save data with it --->
<section data-state="fiji8"><style>.fiji8 header:after { content: "Bioformats"; }</style>
<p>What is bioformats</p>
</section>
<section data-state="fiji8"><style>.fiji8 header:after { content: "Bioformats"; }</style>
<p>Formats - what if it doesn't work for my files?</p>
</section>
<section data-state="fiji8"><style>.fiji8 header:after { content: "Bioformats"; }</style>
<p>Drag and drop vs Bioformats importer</p>
</section>
<section data-state="fiji8"><style>.fiji8 header:after { content: "Bioformats"; }</style>
<p>Bioformats exporter</p>
</section>
<!--Fourth subsession - Practical: opening images with Bioformats, setting calibration, creating scale bars --->
</div> <!-- ---------------------- END OF SLIDES -------------------------- -->
</div>
<!-- Footer -->
<img style="position:fixed;bottom:1em;right:1em;" src="img/logo_WMS.jpg" width="10%">
<!--img style="position:fixed;bottom:1em;left:1em;" src="img/logo_tw.png" width="20%"-->
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<script>
// More info about config & dependencies:
// - https://github.com/hakimel/reveal.js#configuration
// - https://github.com/hakimel/reveal.js#dependencies
Reveal.initialize({
controls: false,
slideNumber: true, //-- Added for development
dependencies: [
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</body>
</html>