-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathproject01.html
More file actions
135 lines (123 loc) · 5.62 KB
/
project01.html
File metadata and controls
135 lines (123 loc) · 5.62 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
<!DOCTYPE HTML>
<!--
Phantom by HTML5 UP
html5up.net | @ajlkn
Free for personal and commercial use under the CCA 3.0 license (html5up.net/license)
-->
<html>
<head>
<link href="./images/pic01_1.png" rel="icon">
<title>Cell Segmentation</title>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1, user-scalable=no" />
<link rel="stylesheet" href="assets/css/main.css" />
<noscript>
<link rel="stylesheet" href="assets/css/noscript.css" />
</noscript>
</head>
<body class="is-preload">
<!-- Wrapper -->
<div id="wrapper">
<!-- Header -->
<header id="header">
<div class="inner">
<!-- Logo -->
<a href="index.html" class="logo">
<span class="symbol"><img src="images/logo.svg" alt="" /></span><span class="title">Project</span>
</a>
<nav>
<ul>
<li><a href="#menu">Menu</a></li>
</ul>
</nav>
</div>
</header>
<!-- Menu -->
<nav id="menu">
<h2>Main Projects</h2>
<ul>
<li><a href="index.html">Home</a></li>
<li><a href="project01.html">Cell Segmentation</a></li>
<li><a href="project02.html">Epigenetic Reprogramming</a></li>
<li><a href="project03.html">Cancer Immune Interaction</a></li>
<!-- <li><a href="project04.html">Equations of Mathematical Physics</a></li> -->
</ul>
</nav>
<!--
<nav id="menu">
<h2>Menu</h2>
<ul>
<li><a href="index.html">Home</a></li>
<li><a href="generic.html">Ipsum veroeros</a></li>
<li><a href="generic.html">Tempus etiam</a></li>
<li><a href="generic.html">Consequat dolor</a></li>
<li><a href="elements.html">Elements</a></li>
</ul>
</nav> -->
<!-- Main -->
<div id="main">
<div class="inner">
<h1>Realize and Optimize Cell Segmentation in Spatial Transcriptomics</h1>
<span class="image main"><img src="images/project1.gif" alt="" /></span>
<p>This work has been presented in the Conference of Academic Communication for Talented Programs
(基础学科英才班学术交流会)<a href="https://news.ustc.edu.cn/info/1055/79508.htm">(news report about this
event)</a> at University of Science and Technology of China. <a
href="./assets/files/presentation_of_cell_segmentation_Yang.pptx"><strong>Slides</strong></a><a
href="https://docs.google.com/presentation/d/1usMTEwL6TOs-pja9dxk3eEhiA2eqDp8G/edit?usp=sharing&ouid=101995205708342383820&rtpof=true&sd=true">Slides
in Google Drive</a>.</p>
<p>Cell segmentation is an important step in the pre-processing of the spatial transcriptomics data.
Nowadays the technologies of spatial transcriptomics can be mainly classified as two types: Based on
NGS and based on image. For these methods that using image to detect the signal of molecular
(probe), we need to assign each signal (point at the image) to a given cell. The cell boundary can
be marked using H&E staining. </p>
<p>After assign the signal to the cell, the data becomes "single cell transcriptomics data with the
position". Then the data can be used to analysis using the standard workflow of single-cell
analysis. </p>
<p>However, in May. 2021, when I start the project, the cell segmentation tools are not optimal. The
most commonly used methods are based on the watershed algorithm, which is not suitable for the tools
developed by our lab</p>
<p>Being new in the computational field, I had a lot to learn. But I successfully utitalized three tools
based on deep learning to our own dataset. In the process I rewrite and rearrange large part of the
source code, which utimately significantly improved the accuracy of cell segmentation in our
dataset. </p>
<p>Another problem in the spatial transcriptomics upstream analysis is to make use of the 3D image. The
format of the data is <a
href="https://docs.openmicroscopy.org/ome-model/5.6.3/ome-tiff/">OME-TIFF</a>. How to use the
image data from different focus plane (z-stacks)? Currently, the most useful method is the maxiumn
intensity projection, but it do not use the signal from all z-stacks.
With the help of colleagues, we developed an algorithm to track the same segmented cell in different
z-stacks. This algorithm has the promise to utilize all information from the image data.</p>
</div>
</div>
<!-- Footer -->
<footer id="footer">
<div class="inner">
<section>
<h2>Follow</h2>
<ul class="icons">
<!-- <li><a href="#" class="icon brands style2 fa-twitter"><span class="label">Twitter</span></a></li>
<li><a href="#" class="icon brands style2 fa-facebook-f"><span class="label">Facebook</span></a></li>
<li><a href="#" class="icon brands style2 fa-instagram"><span class="label">Instagram</span></a></li>
<li><a href="#" class="icon brands style2 fa-dribbble"><span class="label">Dribbble</span></a></li> -->
<li><a href="https://github.com/Nimarkce" class="icon brands style2 fa-github"><span
class="label">GitHub</span></a></li>
<!-- <li><a href="#" class="icon brands style2 fa-500px"><span class="label">500px</span></a></li> -->
<li><a href="mailto:Yang_Li@hms.harvard.edu" class="icon solid style2 fa-envelope"><span
class="label">Email</span></a></li>
</ul>
</section>
<ul class="copyright">
<li>© 2022. All rights reserved</li>
<li></li>
</ul>
</div>
</footer>
</div>
<!-- Scripts -->
<script src="assets/js/jquery.min.js"></script>
<script src="assets/js/browser.min.js"></script>
<script src="assets/js/breakpoints.min.js"></script>
<script src="assets/js/util.js"></script>
<script src="assets/js/main.js"></script>
</body>
</html>