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Colours.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>
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<!-- 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>Channels, Colours, LUTs</h2>
<h4>Erick Martins Ratamero<br>Research Fellow</h4>
</section>
<!--First subsession - Practical: channel display modes, split/merge --->
<section data-menu-title="Channel Display Modes" data-state="fiji6"><style>.fiji6 header:after { content: "Channel Display Modes"; }</style>
<ul style="font-size:80%"><li>Open <a href="material/06-multichannel.tif"><code>06-MultiChannel.tif</code></a></li>
<li>(If opening via URL run <code>[Image > Hyperstacks > Stack to Hyperstack]</code>)</li>
<li>Navigate through the channels then run Channels Tool <code>[Image > Color > Channels Tool]</code> and change to Greyscale</li></ul>
<img class="half" src="img-ia/modes_01.png"/>
<img data-fragment-index="1" class="half fragment" src="img-ia/modes_03.png"/>
<p>In this image, each channel already has an associated Look Up Table (LUT)</p>
</section>
<section data-state="fiji6"><style>.fiji6 header:after { content: "Channel Display Modes"; }</style>
<p>Change to Composite mode</p>
<img class="half" src="img-ia/modes_02.png"/>
<ul class="half">
<li>Use the check boxes (channels tool) to turn channels off</li>
<li>Navigate through the channels. What happens?</li>
<li>Adjust the Black and White Points <code>[Image > Adjust > Brightness & Contrast]</code></li>
<li>Draw a ROI on a bright area and Measure ('m')</li>
</ul>
<p class="fragment">IMPORTANT! The nav bar still <i>selects</i> the active channel, and that is where measurements / maniplulations are applied!</p>
<p class="fragment">The infobar text, slider and 1px coloured image border all indicate which channel is selected.</p>
</section>
<!-- ---------------------- SPLIT/MERGE GOES HERE -------------------------- -->
<!--Second subsession - composite mode, LUTs --->
<section data-state="fiji7"><style>.fiji7 header:after { content: "Colour"; }</style>
<p>Colour in your images is (almost always) dictated by arbitrary lookup tables</p>
<img class="half" src="img-ia/colour_02.png"/>
<img data-fragment-index="1" class="third fragment" src="img-ia/colourLUT1.png"/>
<p class="fragment" data-fragment-index="1">Lookup tables (LUTs) translate an intensity (1-256 for 8 bit) to an RGB display value</p>
</section>
<section data-state="fiji7"><style>.fiji7 header:after { content: "Colour"; }</style>
<p>Colour in your images is (almost always) dictated by arbitrary lookup tables</p>
<img class="third" src="img-ia/colourLUT2.png"/>
<img data-fragment-index="1" class="third fragment" src="img-ia/colourLUT3.png"/>
<p>Lookup tables (LUTs) translate an intensity (1-256 for 8 bit) to an RGB display value</p>
</section>
<section data-state="fiji7"><style>.fiji7 header:after { content: "Colour"; }</style>
<p>You can use whatever colours you want (they are arbitrary after all), but the most reliable contrast is greyscale</p>
<img src="img-ia/colour_05.png"/>
<p class="subtle">More info on colour and sensitivity of the human eye <a href="https://postacquisition.wordpress.com/2015/04/15/see-the-world-in-black-and-white/" target="_blank">here</a></p>
<!-- <ol><li>Combinations for multichannel images</li><li>Colour Blindness</li></ol> -->
</section>
<section data-state="fiji8"><style>.fiji8 header:after { content: "Colour: Combinations"; }</style>
<p>Additive and Subtractive Colours can be mixed in defined ways</p>
<img class="half" src="img-ia/colour_06.png"/>
<p>Non 'pure' colours cannot be combined in reliable ways (as they contain a mix of other channels)
</section>
<section data-state="fiji8"><style>.fiji8 header:after { content: "Colour: Combinations"; }</style>
<p>BUT! Interpretation is <i>highly</i> context dependent!</p>
<a href="https://twitter.com/dn_mason/status/1034380257451810816" target="_blank"><img class="third" src="img-ia/colour_07.png"/></a><img class="third" src="img-ia/colour_08.png"/><img data-fragment-index="1" class="third fragment" src="img-ia/colour_11.png"/>
<p data-fragment-index="1" class="fragment"><a href="https://en.wikipedia.org/wiki/The_dress">https://en.wikipedia.org/wiki/The_dress</a></p>
</section>
<section data-state="fiji8b"><style>.fiji8b header:after { content: "Colour: R/G Colour blindness"; }</style>
<p>~10% of the population have trouble discerning Red and Green. Consider using Green and Magenta instead which still combine to white.</p>
<img src="img-ia/colour_10.png"/>
</section>
<!--Third subsession - practical: play with LUTs --->
<section data-state="fiji14a"><style>.fiji14a header:after { content: "Colour: Changing LUTs"; }</style>
<div class="twothirds left" style="font-size:90%">
<ul><li>Open <a href="material/06-multichannel.tif"><code>06-MultiChannel.tif</code></a></li>
<li>(If opening via URL run <code>[Image > Hyperstacks > Stack to Hyperstack]</code>)</li>
<li>Run <code>[Image > Lookup Tables]</code>, try a few different ones</li>
<li>Run Channels Tool <code>[Image > Color > Channels Tool]</code>, make sure you're in Color or Composite mode, hit More, select a LUT</li>
<li data-fragment-index="1" class="fragment">Run <code>[Image > Color > Display LUTs]</code> to see all the LUTs on your version of Fiji</li></ul>
<img data-fragment-index="1" class="fragment twothirds" src="img-ia/colourLUT6.png"/>
</div>
<img class="third right" src="img-ia/colourLUT5.png"/>
</section>
<section data-state="fiji14a"><style>.fiji14a header:after { content: "Colour: Changing LUTs"; }</style>
<p>A couple of useful LUTs:</p>
<img class="threequart" src="img-ia/colourLUT7.png"/>
</section>
<!--Fourth subsession - RGB images and montages --->
<!--NOT MY EXPERTISE - CAN SOMEONE ELSE FILL IT IN? --->
<!--Fifth subsession - practical: from multichannel to split + sync windows and montage--->
<!--NOT MY EXPERTISE - CAN SOMEONE ELSE FILL IT IN? --->
</div> <!-- ---------------------- END OF SLIDES -------------------------- -->
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