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<!DOCTYPE html>
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<title>Reference Materials — W. M. Keck Microscopy Center</title>
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<h1>Reference Materials</h1>
<p>Guides, protocols, software resources, and training materials for facility users</p>
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<div class="doc-head"><h2>Getting started</h2></div>
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<p>Whether you are new to the facility or looking to expand your imaging repertoire, these materials are a starting point. Contact us for instrument-specific documentation or to request a custom protocol.</p>
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<div class="resource-card">
<div class="rc-tag">Fundamentals</div>
<h3>Microscopy Fundamentals Guide</h3>
<p>Introduction to light microscopy principles, optical sectioning, and fluorescence. Recommended reading before a first training session.</p>
<ul class="rc-links">
<li><a href="https://www.ibiology.org/online-biology-courses/microscopy-series/" target="_blank" rel="noopener">iBiology Microscopy Course →</a></li>
<li><a href="https://www.microscopyu.com/" target="_blank" rel="noopener">Nikon MicroscopyU →</a></li>
</ul>
</div>
<div class="resource-card">
<div class="rc-tag">Protocols</div>
<h3>Sample Preparation Handbook</h3>
<p>Fixation, staining, and mounting protocols for common biological samples. Includes recommendations for each instrument in the facility.</p>
<ul class="rc-links">
<li><a href="https://www.leica-microsystems.com/science-lab/life-science/how-to-prepare-specimen-for-immunofluorescence-microscopy/" target="_blank" rel="noopener">Preparing specimens for immunofluorescence (Leica) →</a></li>
<li><a href="https://imb.uq.edu.au/facilities/microscopy/2020-microscopy-resources/sample-prep/fixing-and-labelling-cells-immunofluorescence-if-microscopy" target="_blank" rel="noopener">Fixing & labelling cells for IF (UQ IMB) →</a></li>
</ul>
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<div class="resource-card">
<div class="rc-tag">Equipment</div>
<h3>Instrument-Specific Tutorials</h3>
<p>Step-by-step setup guides for the Leica SP8X, Zeiss 880, Leica Widefield, and IMARIS workstation — including acquisition parameter templates.</p>
<ul class="rc-links">
<li><a href="https://www.leica-microsystems.com/science-lab/" target="_blank" rel="noopener">Leica Science Lab tutorials →</a></li>
<li><a href="https://www.youtube.com/watch?v=8o_j0N385g0" target="_blank" rel="noopener">Leica SP8X video tutorial (YouTube) →</a></li>
<li><a href="https://media.bcm.edu/documents/2018/43/oivm-lsm880-user-guide.pdf" target="_blank" rel="noopener">ZEISS LSM 880 training guide (PDF) →</a></li>
<li><a href="https://imaris.oxinst.com/tutorials" target="_blank" rel="noopener">IMARIS video tutorials →</a></li>
</ul>
</div>
<div class="resource-card">
<div class="rc-tag">Advanced</div>
<h3>Advanced Imaging Techniques</h3>
<p>Resources on FRAP, FRET, spectral unmixing, live-cell timelapse, and mosaic tiling strategies.</p>
<ul class="rc-links">
<li><a href="https://www.leica-microsystems.com/science-lab/life-science/step-by-step-guide-for-frap-experiments/" target="_blank" rel="noopener">Step-by-step FRAP guide (Leica) →</a></li>
<li><a href="https://www.microscopyu.com/applications/fret" target="_blank" rel="noopener">FRET microscopy (MicroscopyU) →</a></li>
<li><a href="https://www.leica-microsystems.com/science-lab/life-science/spectral-detection-how-to-define-the-spectral-bands-that-collect-probe-specific-emission/" target="_blank" rel="noopener">Spectral detection (Leica) →</a></li>
<li><a href="https://www.microscopyu.com/applications/live-cell-imaging" target="_blank" rel="noopener">Live-cell imaging (MicroscopyU) →</a></li>
</ul>
</div>
<div class="resource-card">
<div class="rc-tag">Analysis</div>
<h3>Image Analysis Guide</h3>
<p>Tutorials for IMARIS (3D/4D), Fiji/ImageJ, and common analysis workflows including segmentation, particle tracking, and co-localization.</p>
<ul class="rc-links">
<li><a href="https://bioimagebook.github.io/" target="_blank" rel="noopener">Introduction to Bioimage Analysis →</a></li>
<li><a href="https://imagej.net/learn/" target="_blank" rel="noopener">ImageJ / Fiji documentation →</a></li>
<li><a href="https://imaris.oxinst.com/tutorials" target="_blank" rel="noopener">IMARIS tutorials →</a></li>
</ul>
</div>
<div class="resource-card">
<div class="rc-tag">Data Management</div>
<h3>Data Management Best Practices</h3>
<p>File naming conventions, metadata standards, directory structure recommendations, and archival guidance for microscopy datasets.</p>
<ul class="rc-links">
<li><a href="https://quarep.org/" target="_blank" rel="noopener">QUAREP-LiMi standards →</a></li>
<li><a href="https://www.openmicroscopy.org/" target="_blank" rel="noopener">Open Microscopy Environment (OME) →</a></li>
<li><a href="https://lib.uw.edu/research-services/data-services/" target="_blank" rel="noopener">UW Libraries Data Services →</a></li>
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