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ColemanHarris20210414
(07 Apr 2021,
AndrewSpieker
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%HEAD{ NAME="Coleman Harris" AFFILIATION="Vanderbilt University Medical Center" TITLE="Combining batches of high-dimensional multiplexed images" IMAGELINK="https://cdn.vanderbilt.edu/vu-wp0/wp-content/uploads/sites/190/2017/11/05144334/3D8B6715-80C6-42C0-B7FA-072E8E29240E-e1536159157954.jpeg" }% High-dimensional multiplexed imaging methods can help quantify the heterogeneity of cell populations in healthy and tumorous tissues, offering insight into tumor progression and improved treatment strategies. However, implicit biases exist in the imaging pipeline - images are distorted by optical effects, slide and batch effects, and instrument variability. Normalization of this data is compounded by the number of markers and natural tissue variability within each image, introducing systematic differences that impact inference. In this work, we introduce an image normalization pipeline to reduce systematic variability in multiplexed images by correcting for batch effects. We build on existing methods to compare the following approaches to correct for the batch effects in the data: a logarithmic transformation, a simple standardization (division by the mean), and two approaches using functional data registration. We demonstrate these methods by analyzing multiplexed immunofluorescence (MxIF) images of human colorectal tissue samples to quantify the reduction in variability of the data, namely using thresholding methods and random effects models. We further demonstrate the method's ability to retain biological signal by evaluating prediction accuracy of models for specific regions containing tumors in the tissue samples. %TAIL{DATE="14 April 2021"}% <!-- * Set HEAD = <div class="w3-card-2" id="task" style="max-width:750px; margin-left: 0px;"> <header class="w3-container w3-blue" style="padding:40px"><h1>Biostatistics Weekly Seminar</h1><br><h2 style="color:white;">%TITLE%<br><br>%NAME%<br>%AFFILIATION%</h2></header><div class="w3-container" style="padding:40px"><IMG SRC=%IMAGELINK% align="left" id="mug"/> * Set TAIL = <br><h3>Zoom (Link to Follow)<br>%DATE%<br>1:30pm</h3></div></div><br> --> <style> .w3-card-2,.w3-example{box-shadow:0 2px 4px 0 rgba(0,0,0,0.16),0 2px 10px 0 rgba(0,0,0,0.12)!important} .w3-blue,.w3-hover-blue:hover{color:#fff!important;background-color:#2196F3!important} .w3-container{padding:0.01em 16px} .foswikiTopic {font-family: 'Open Sans', sans-serif;} /* Removes location hierarchy (usually written in grey text) */ .patternHomePath {display:none;} /* Removes bar with edit and attach buttons and location hierarchy */ .patternTop{display:none;} h1, h2, h3, h4, h5, h6{font-family: 'Montserrat','Open Sans', sans-serif;font-weight:700;} h1, h2, h3, h4, h5, h6{color:#bf1735;} h1:first-of-type{color:#2a3e6e;margin-bottom:25px;margin-top:5px;} .foswikiImage{margin-left:-9px;} img#mug{padding-right: 40px; padding-bottom:25px; height:250px;} </style>
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Topic revision: r1 - 07 Apr 2021,
AndrewSpieker
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