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index.html
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<!DOCTYPE html>
<html lang="en">
<head>
<link rel="icon" type="image/x-icon" href="https://cdn.glitch.global/5fbfde84-4f5e-46c9-b02b-7de045bf80b7/favicon.ico?v=1664757688575">
<title>IC@Y Cell Counter</title>
<!-- Import the webpage's stylesheet -->
<link rel="stylesheet" href="css/style.css" />
<!-- Import the webpage's javascript file -->
<script src="js/tabs.js" defer></script>
<script src="js/utils.js" defer></script>
<script src="js/script.js" defer></script>
<script src="js/imagefilters.js" defer></script>
<script src="js/keyBoardControls.js" defer></script>
<script src="js/simpleStatistics.js" defer></script>
<script src="js/count.js" defer></script>
<script src="js/openCvPredictions.js" defer></script>
<script src="js/openCvBlobDataCollection.js" defer></script>
<script>
</script>
</head>
<body>
<!-- <h2>IC@Y Cell Counter</h2> -->
<video autoplay></video>
<div id="container">
<div class="tab">
<button class="tablinks" id="defaultOpen" onclick="openTab(event, 'Manual')">Count</button>
<button class="tablinks" onclick="openTab(event, 'Capture')">Capture</button>
<button class="tablinks" onclick="openTab(event, 'Automatic')">Data Collection</button>
</div>
<div id="Manual" class="tabcontent">
<span onclick="this.parentElement.style.display='none'" class="topright">×</span>
<h3>Automatic & Manual Counter</h3>
<p>Get cell counts from a sample using the automatic and/or manual counters.</p>
<div class="slidecontainer">
<b> Box Length: <span id="demo"></span></b>
<input id="boxLength" type="range" min="0" max="768" value="470">
<b> Default: (470) </b>
<p>
<b>
Boxes Counted: <span id="boxesAuto">0</span>
</b>
</p>
</div>
<script>
var slider = document.getElementById("boxLength");
var output = document.getElementById("demo");
output.innerHTML = slider.value;
slider.oninput = function() {
output.innerHTML = this.value;
}
</script>
<h5>Manual Counts</h5>
<table id="manualTable">
<tr>
<th>Live Cells (J)</th>
<th>Budding Cells (K)</th>
<th>Dead Cells (L)</th>
<th>Total Cells</th>
<th>Viability</th>
</tr>
<tr id="manualValues">
<td id="liveManual">0</td>
<td id="buddingManual">0</td>
<td id="deadManual">0</td>
<td id="totalManual">0</td>
<td id="viabilityManual">0</td>
<td><button class="copy-btn countButton">Copy</button></td>
</tr>
</table>
<!-- <button class="countButton" onclick="estimateCounts()">
Count
</button> -->
<hr>
<h5>Automatic Counts</h5>
<p>
<button class="countButton" onclick='estimateCounts()'>Count</button>
<button class="countButton" onclick='resetCounts()'>Reset</button>
<a href="#ex1" rel="modal:open">
<button class="countButton" id="preview" onclick="previewCounts() ">Preview</button>
</a>
</p>
<table>
<tr>
<th>Live Cells</th>
<th>Budding Cells</th>
<th>Dead Cells</th>
<th>Total Cells</th>
<th>Viability</th>
</tr>
<tr id="autoValues">
<td id="liveAuto">0</td>
<td id="buddingAuto">0</td>
<td id="deadAuto">0</td>
<td id="totalAuto">0</td>
<td id="viabilityAuto">0</td>
<td><button class="copy-btn countButton">Copy</button></td>
</tr>
</table>
<p></p>
<table>
<tr>
<th>Total Accuracy</th>
<th>Viability Accuracy</th>
<th>Budding Accuracy</th>
</tr>
<tr id="resultsValues">
<td id="totalAccuracy">0</td>
<td id="viabilityAccuracy">0</td>
<td id="buddingAccuracy">0</td>
<td><button class="copy-btn countButton">Copy</button></td>
</tr>
</table>
</div>
<div id="Capture" class="tabcontent">
<span onclick="this.parentElement.style.display='none'" class="topright">×</span>
<h3>Capture Images</h3>
<p>Click the capture button below to take pictures during an experiment</p>
<p>
<button class="countButton" id="captureButton" onclick="capture()">Capture</button>
<!-- <button class="countButton" onclick='resetAuto()'>Reset</button> -->
</p>
</div>
<div id="Automatic" class="tabcontent">
<span onclick="this.parentElement.style.display='none'" class="topright">×</span>
<h3>Automatic Counter Data Collection</h3>
<p>This is a section to gather data for mathematically characterising yeast cells</p>
<p>Prepare a clean yeast sample to run testing with. Then press B to generate parameters</p>
<button class="countButton" id="dataCollect">Collect</button>
<table>
<tr>
<th>Median Circularity</th>
<th>Stdev Circularity</th>
<th>Median Inertia</th>
<th>Stdev Inertia</th>
<th>Median Convexity</th>
<th>Stdev Convexity</th>
</tr>
<tr>
<td id="medianCircularity">0</td>
<td id="stdevCircularity">0</td>
<td id="medianInertia">0</td>
<td id="stdevInertia">0</td>
<td id="medianConvexity">0</td>
<td id="stdevConvexity">0</td>
</tr>
</table>
<h5>Yeast Blob Data Array:</h5>
<!-- <p id="blobData"></p> -->
<textarea id="blobData"></textarea>
</div>
<div id="canvasBox">
<img src="images/map/1.png" id="map">
<div id="instructions">
<h5>Instructions</h5>
<p>Automatic counts can be taken by pressing (Enter) on your keyboard or just clicking 'Count'</p>
<p>( If manual counts are needed to compare counter precision or just personal use) press the appropriate keys for the specific cell type:</p>
<p>J (Live), K (Budding), L (Dead), R (Reset)</p>
<p>Once you complete the manual count, press enter to perform the automatic count (only press enter after finishing manual count)</p>
<p>Record the Counts and accuracies in the microscope testing file for that day</p>
</div>
<p>
<canvas id="canvasInput"></canvas>
</p>
<!-- <p>
</p> -->
<div id="ex1" class="modal">
<h3>Cell Counter Preview</h3>
<canvas id="canvasOutput"></canvas>
</div>
</div>
</div>
<!-- <canvas id="canvasInput"></canvas>
<canvas id="canvasOutput"></canvas> -->
<script src ="js/opencv/opencv.js"></script>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.6.0/jquery.min.js"></script>
<!-- <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.0.0/jquery.min.js"></script> -->
<!-- jQuery Modal -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery-modal/0.9.1/jquery.modal.min.js"></script>
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/jquery-modal/0.9.1/jquery.modal.min.css" />
<!-- <script async src="https://docs.opencv.org/3.4.0/opencv.js" type="text/javascript"></script> -->
</body>
</html>