Difference between revisions of "Team:Peking/Software"

 
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<html>
+
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−
 
+
<!--[if IE 8 ]><html class="no-js ie ie8" lang="en"> <![endif]-->
−
<head>
+
<!--[if (gte IE 8)|!(IE)]><!-->
−
<style>
+
<html class="no-js" lang="en">
−
             #home_logo, #sideMenu {
+
    <!--<![endif]-->
−
             display: none;
+
    <head>
 +
        <!--- Basic Page Needs========================================================================= -->
 +
        <meta charset="utf-8"/>
 +
        <title></title>
 +
        <meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.2, user-scalable=yes" />
 +
        <meta name="description" content="Wiki of Peking iGEM 2018" />
 +
        <meta name="author" content="Peking iGEM"/>
 +
        <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 +
        <!-- Mobile Specific Metas===================================================================== -->
 +
        <meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1"/>
 +
        <!-- Fix  Overwrite the original iGEM style=================================================== -->
 +
        <link href="https://2018.igem.org/Template:Peking/css/fix?action=raw&ctype=text/css" rel="stylesheet" />
 +
        <!-- CSS======================================================================================= -->
 +
        <link href="https://2018.igem.org/Template:Peking/css/bootstrap_min?action=raw&ctype=text/css" rel="stylesheet" />
 +
        <link href="https://2018.igem.org/Template:Peking/css/style?action=raw&ctype=text/css" rel="stylesheet" />
 +
        <!-- CSS======================================================================================= -->
 +
        <link rel="stylesheet" href="https://2018.igem.org/Template:Peking/css/default?action=raw&ctype=text/css"/>
 +
        <link rel="stylesheet" href="https://2018.igem.org/Template:Peking/css/layout?action=raw&ctype=text/css"/>
 +
        <link rel="stylesheet" href="https://2018.igem.org/Template:Peking/css/media-queries?action=raw&ctype=text/css"/>
 +
        <link rel="stylesheet" href="https://2018.igem.org/Template:Peking/css/notebook_panel?action=raw&ctype=text/css"/>
 +
        <style>
 +
                        body { background: #D2D8D8 url(https://static.igem.org/mediawiki/2018/7/78/T--Peking--images_bodyBackground.jpeg); background-attachment:fixed;}
 +
             .texttitle{
 +
                color:#6495ED;
 +
                font-size: 32px;
 +
                line-height: 48px;
 +
                margin-bottom: 12px;
 +
                font-family: raleway-bold, sans-serif !important;
 +
                background: transparent;
 +
                letter-spacing: 3px;
 +
                text-transform: uppercase;
 +
                font-weight: 350;
 +
                text-align: center;
 +
                padding-top:40px;
 +
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 +
        sup{font-size:11px;}
 +
        .references{margin-top:150px;margin-bottom:40px;}
 +
        .references p{font-size:14px !important; color:#666161 !important;}
 +
        .classic-title {font-weight: 300;padding-top:30px;}
 +
        .classic-title span {
 +
            padding-bottom: 8px;
 +
            border-bottom: 1px solid #383232;
 +
             font-weight: 400;
 
         }
 
         }
−
 
+
        figure{margin-top:40px;margin-bottom:40px;height:auto;}
−
         #sideMenu, #top_title, .patrollink {
+
         .anchor{padding-top:100px;margin-top:-100px;}
−
             display: none;
+
             </style>
 +
       
 +
    </head>
 +
    <body>
 +
        <!--sidebar 引用==============================================================================-->
 +
        <style>
 +
            #primary span{
 +
                display:block;
 +
                word-break:break-all
 +
            }
 +
       
 +
        #page-wrap {
 +
            width: 25%;
 +
            margin: 0px;
 +
            position: relative;
 
         }
 
         }
−
 
+
         #page-wrap a:hover {color:#6495ED;}
−
         #content {
+
       
−
            width: 100%;
+
        #sidebar {
−
            padding: 0px;
+
             width: 25%;
−
             margin-top: 0px;
+
 
             margin-left: 0px;
 
             margin-left: 0px;
−
            margin-right: 0px;
 
 
         }
 
         }
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+
         @media (min-width:1024px){
−
         body {
+
             #sidebar{position:relative;top:120px;max-width:200px;}}
−
             background-color: #FAFAFA;
+
         @media (max-width: 1023px){
−
         !important;
+
            #sidebar{display:none;
 +
            }
 +
            #page-wrap{display:none;}
 
         }
 
         }
−
 
+
        </style>
−
         #bodyContent h1, #bodyContent h2, #bodyContent h3, #bodyContent h4, #bodyContent h5 {
+
          
−
             margin-bottom: 0px;
+
       
 +
        <script type="text/javascript">
 +
            function menuFixed(id){
 +
                var obj = document.getElementById(id);
 +
                var _getHeight = obj.offsetTop;
 +
               
 +
                window.onscroll = function(){
 +
                    changePos(id,_getHeight);
 +
                }
 +
            }
 +
        function changePos(id,height){
 +
            var obj = document.getElementById(id);var windowBottom = $(window).scrollTop() + $(window).innerHeight();
 +
            if(w>=1024){
 +
                if($(window).scrollTop() + $(window).height() > $(document).height() - 230){
 +
                    $('#sidebar').fadeOut("fast");}else{$('#sidebar').fadeIn("fast");}
 +
            }
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            var scrollTop = document.documentElement.scrollTop || document.body.scrollTop -230;
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            var windowBottom = $(window).scrollTop() + $(window).innerHeight();
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            var w = window.innerWidth;
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 +
            if(scrollTop < height){ obj.style.position = 'relative';
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            }else{
 +
                obj.style.position = 'fixed';
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            }
 +
        }
 +
        </script>
 +
       
 +
        <script type="text/javascript">
 +
            window.onload = function(){
 +
                menuFixed('sidebar');
 +
            }
 +
        </script>
 +
        <script>
 +
            function naver(id){
 +
                var obj=document.getElementById(id);
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                var oPos=obj.offsetTop;
 +
                return window.scrollTo(0,oPos+250);
 +
            }
 +
        </script>
 +
        <!--sidebar 引用 end ==============================================================================-->
 +
        <!--panel 引用==================================================================================-->
 +
        <style type="text/css">
 +
            .panel-default .panel-heading a{
 +
                text-decoration: none;
 +
                display:block;
 +
                padding:10px;
 +
            }
 +
        .panel-heading.panel-title{
 +
            text-decoration: none;
 +
            padding-top:0px;
 +
            padding-bottom:0px;
 +
            padding-left:0px;
 +
            padding-right:0px;
 +
            text-align:center;
 +
            font-size:19px;
 +
           
 +
        }
 +
        a[aria-expanded="true"] {
 +
            background-color:rgba(70, 73, 76, 0.95);
 +
            text-decoration: none;
 +
            color:white;
 +
        }
 +
       
 +
        .panel-default .panel-heading a[aria-expanded="false"]{
 +
            -o-transition: background-color 1s linear;
 +
            -moz-transition: background-color 1s linear;
 +
            -khtml-transition: background-color 1s linear;
 +
            -webkit-transition: background-color 1s linear;
 +
            -ms-transition: background-color 1s linear;
 +
            transition: background-color 1s linear;
 +
        }
 +
        .panel-default .panel-heading a[aria-expanded="false"]:hover{
 +
            background-color:rgba(70, 73, 76, 0.95);
 +
            text-decoration: none;
 +
            color:white;
 +
        }
 +
        .panel-default .panel-heading a[aria-expanded="true"]{
 +
            -o-transition: opacity 1s linear;
 +
            -moz-transition: opacity 1s linear;
 +
            -khtml-transition: opacity 1s linear;
 +
            -webkit-transition: opacity 1s linear;
 +
            -ms-transition: opacity 1s linear;
 +
            transition: opacity 0.7s linear;
 +
        }
 +
        .panel-default .panel-heading a[aria-expanded="true"]:hover{
 +
            opacity:0.7;
 +
        }
 +
       
 +
        .coll p a{
 +
            color:#6495ED !important;
 +
        }
 +
        .coll p a:hover{
 +
            color:#6495ED!important;
 +
        }
 +
        .coll {
 +
            width:100%;
 +
            float:left;
 +
        }
 +
        .coll .info {
 +
            width:6%;
 +
            font-size:11px;
 +
            color:#a4a4a4;
 +
             margin-top:0px;
 +
            float:left;
 +
           
 +
        }
 +
        .coll .content {
 +
            width:94%;
 +
            float:left;
 +
            margin-left:40px;
 +
            margin-top:-3px;
 +
        }
 +
        .coll .ordi {
 +
            width;100%;
 +
            margin:0px 0px 0px 0px;
 +
            font-size:35px;
 +
            font-style:italic;
 +
            float:left;
 +
            color:#1E90FF;
 +
            opacity:0.8;
 
         }
 
         }
−
a:link {
+
       
−
                        text-decoration: none;
+
            </style>
−
                    }
+
       
 +
        <script type="text/javascript">
 +
            $(document).ready(function(){
 +
                              $("#button1").click(function(){
 +
                                                  $(".panel-collapse").collapse("show");
 +
                                                  });
 +
                              });
 +
                              $(document).ready(function(){
 +
                                                $("#button2").click(function(){
 +
                                                                    $(".panel-collapse").collapse("hide");
 +
                                                                    });
 +
                                                });
 +
                                                $("#notebook").addClass("navbar-active");
 +
            </script>
 +
        <!--panel 引用 end ==================-->
 +
       
 +
          <!-- Navigation -->
 +
        <div id="navigation" class="navbar navbar-fixed-top">
 +
            <div class="navbar-inner ">
 +
                <div class="container no-padding">
 +
                    <a class="show-menu" data-toggle="collapse" data-target=".nav-collapse"><span class="show-menu-bar"></span>
 +
                    </a>
 +
                    <div id="logo" style="max-width:0px"><a class="" href="https://2018.igem.org/Team:Peking"><img
 +
                    src="https://static.igem.org/mediawiki/2018/3/36/T--Peking--Logo.png"></a></div>
 +
                 
 +
                    <div class="nav-collapse collapse">
 +
                        <ul class="nav">                         
  
−
                    a:visited {
+
                            <li class="menu-1"><a class="colapse-menu1" href="https://2018.igem.org/Team:Peking">Home</a>
−
                        text-decoration: none;
+
                            </li>
−
                    }
+
  
−
                    a:active {
+
                            <li class="dropdown menu-2"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Project</a>
−
                        text-decoration: none;
+
                                <ul class="dropdown-menu">
−
                    }
+
                                    <li><a href="https://2018.igem.org/Team:Peking/Project" class="barfont1">Description</a></li>
 +
                                    <li><a href="https://2018.igem.org/Team:Peking/Design" class="barfont1">Design</a></li>
 +
                                    <li><a href="https://2018.igem.org/Team:Peking/Demonstrate" class="barfont1">Demonstration</a></li>
 +
                                    <li><a href="https://2018.igem.org/Team:Peking/Perspective" class="barfont1">Perspective</a></li>
 +
                                </ul>
 +
                            </li>
 +
                            <li class="menu-3"><a class="colapse-menu1" href="https://2018.igem.org/Team:Peking/Model">Modeling</a>
 +
                            </li>
 +
                            <li class="menu-4"><a class="colapse-menu1" href="https://2018.igem.org/Team:Peking/Software">Software</a>
 +
                            </li>
  
−
                    a:hover {
 
−
                    }
 
−
.dropbtn {
 
−
    background-color: #4CAF50;
 
−
    color: white;
 
−
    padding: 16px;
 
−
    font-size: 16px;
 
−
    border: none;
 
−
    cursor: pointer;
 
−
}
 
  
−
.dropdown {
+
                            <li class="menu-6"><a class="colapse-menu1" href="https://2018.igem.org/Team:Peking/Human_Practices">Human Practices</a>
−
    position: relative;
+
                            </li>
−
    display: inline-block;
+
                                <li class="dropdown menu-7"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Achievement</a>
−
}
+
                                    <ul class="dropdown-menu">
 +
                                        <li><a href="https://2018.igem.org/Team:Peking/Judging_Form" class="barfont1">Judging Form</a></li>
 +
                                        <li><a href="https://2018.igem.org/Team:Peking/Parts" class="barfont1">Parts</a></li>
 +
                                        <li><a href="https://2018.igem.org/Team:Peking/Improve" class="barfont1">Improvement</a></li>
 +
                                        <li><a href="https://2018.igem.org/Team:Peking/InterLab" class="barfont1">InterLab</a></li>
  
−
.dropdown-content {
+
                                    </ul>
−
    display: none;
+
                                </li>
−
    position: absolute;
+
                                <li class="dropdown menu-8"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Lab</a>
−
    background-color: #f9f9f9;
+
                                    <ul class="dropdown-menu">
−
    min-width: 140px;
+
                                        <li><a href="https://2018.igem.org/Team:Peking/Team_Members">Team Members</a></li>
−
    box-shadow: 0px 8px 16px 0px rgba(0,0,0,0.2);
+
                                        <li><a href="https://2018.igem.org/Team:Peking/Attributions" class="barfont1">Attributions</a></li>
−
}
+
                                        <li><a href="https://2018.igem.org/Team:Peking/Notebook" class="barfont1">Notebook</a></li>
 +
                                        <li><a href="https://2018.igem.org/Team:Peking/Collaborations" class="barfont1">Collaborations</a></li>
 +
                                        <li><a href="https://2018.igem.org/Team:Peking/Safety" class="barfont1">Safety</a></li>
 +
                                        <li><a href="https://2018.igem.org/Team:Peking/Acknowledgement" class="barfont1">Acknowledgement</a></li>
 +
                                       
 +
                                    </ul>
 +
                                </li>
 +
                                </div>
 +
                </div>
 +
            </div>
 +
        </div>
 +
        <!--/Navigation -->
 +
       
 +
       
 +
        <!-- Page Title======================================================================== -->
 +
        <div id="page-title">
 +
            <div class="row">
 +
                <div class="twelve columns centered text-center">
 +
                    <h1>Software </h1>
 +
                   
 +
                </div>
 +
            </div>
 +
        </div><!-- Page Title End-->
 +
       
 +
       
 +
        <div id="page-content" class="row page">
 +
            <div id="primary" class="twelve columns">
 +
                <section>
 +
                    <div class="row">
 +
                       
 +
                       
 +
                       
 +
                    <div class="row">
 +
                       
 +
                       
 +
                       
 +
                                <div class="three columns">
 +
                            <div id="page-wrap">
 +
                                <div id="sidebar" style="color:#000000">
 +
                                    <h4><a href="javascript:void(0);" onclick="naver('A')">&bull;Overview</a></h4>
 +
                                    <h4><a href="javascript:void(0);" onclick="naver('B')">&bull;Naming&nbsp;Rules&nbsp;Management</a></h4>
 +
                                    <h4><a href="javascript:void(0);" onclick="naver('C')">&bull;Grayscale&nbsp;&&nbsp;Merge</a></h4>
 +
                   
 +
                                    <h4><a href="javascript:void(0);" onclick="naver('D')">&bull;Video&nbsp;&&nbsp;Z&nbsp;Stacks</a></h4>
 +
                                    <h4><a href="javascript:void(0);" onclick="naver('E')">&bull;Cropping</a></h4>
 +
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                                  &bull;Time&nbsp;Scale&nbsp;&&nbsp;Scale&nbsp;Plate</a></h4>
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<div class="texttitle"> Overview
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                                    <p>We produce abundant fluorescence images in our experiments. However, there are many challenges in the processing of such data, which can be extremely large. Even in the case of 1 hour of imaging for 25 positions at 3 channels every minute, the microscope will yield 4500 high-resolution images. To help with the image processing in such a high throughput, we developed software for microscope image batching(Fig. 1).
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<p style="text-align:justify; text-justify:inter-ideograph">This software was written specifically for the problems we encountered. </p><br/>
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                                    <p>The first problem we met is that the file names of the exported images are generated according to <b>fuzzy rules</b>. Confusingly, the rules for the number of the positions, channels and times vary among files. To address the diversity of file names of images derived from different microscopes, we managed to build a <b>naming rule manager</b> (Fig. 2), which can create and modify the naming rule. The rules that can be made are <b>flexible</b>, and can contain up to 4 variables and 4 customized strings. Every variable has a customized zero filling function that can solve annoying problems such as the numbers 01 to 99. The users can also <b>share</b> their rules in the form of a file, which may benefit group projects.<a href="https://static.igem.org/mediawiki/2018/3/32/T--Peking--Users_manual.pdf"> Please refer to the user manuals for more details.</a>
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                                    <p>After solving the problem of obtaining the files, we can now address their processing.The most important difference between fluorescence microscope images and ordinary photographs is the channel function. We needed to contrast different fluorescence channels to assess the result. However, exporting a great number of large images can be exceedingly time-consuming. Thus, if we can merge the channels or convert the images to grayscale after cropping, we will save much time. Thus, we added the functions of <b>merging</b>(Fig. 3) and <b>grayscale conversion</b> (Fig. 4)to our software first.<a href="https://static.igem.org/mediawiki/2018/3/32/T--Peking--Users_manual.pdf"> Please refer to the user manuals for more details.</a>  </p>
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                                    <p>In living organisms, if we want to show dynamic processes using video recordings, we will need to fuse the images in the correct order to make a video. We therefore wrote functions to <b>export video</b> by time or by z axis.(Fig. 5) <a href="https://static.igem.org/mediawiki/2018/3/32/T--Peking--Users_manual.pdf"> Please refer to the user manuals for more details.</a> </p>
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                                    <p>In scientific research, cropping is widely used to beautify the images and emphasize the target. To meet the need for flexible cropping, we provided two cropping methods. <b>Drawing cropping</b> can draw the range to be cropped while <b>position cropping</b> crops the given position.(Fig. 6) Please refer to the user manuals for more details.  <a href="https://static.igem.org/mediawiki/2018/3/32/T--Peking--Users_manual.pdf"> Please refer to the user manuals for more details.</a></p>
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<div class="texttitle">Fixing Drift and Rotation
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                                    <p>What’s more, sometime the cells float during the process of photographing, which results in the cells drifting or even rotating in the video. We will have to make a larger cropping to ensure that the cell will not move out of the field of view. To solve this problem, we wrote a function that can move the cropping frame with the cell linearly, which can <b>fix the drifting</b> of cells to some extent(Fig. 7). Also, we can rotate the image using the setting before cropping, by which we may also <b>fix the rotation</b> of the cells(Fig. 8). Please refer to the user manuals for more details. <a href="https://static.igem.org/mediawiki/2018/3/32/T--Peking--Users_manual.pdf"> Please refer to the user manuals for more details.</a> </p>
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<p><div align="center">Figure. 7 The videos before and after drift fixing. The yeast are less locomotive after fixing.</div></p>
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<p><div align="center">Figure. 8 The videos before and after rotation and drift fixing, The yeast are less rotational after fixing.</div></p>
  
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              style="color: #000000; font-size: x-large"><strong>Peking iGEM 2018</strong></a>
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                                    <p>Eventually, the micrographs in science need information attached to them before they can be shown to the public. The time scale of every frame and the scale of the cells are the most common features.(Fig. 9) We can add the <b>time scale</b> information to the image by the given position, start time, interval and unit. Furthermore, <b>the scale bar</b>, which indicates the scale of the cells, can be added by the given position, total length, length/pixel and unit.<a href="https://static.igem.org/mediawiki/2018/3/32/T--Peking--Users_manual.pdf"> Please refer to the user manuals for more details.</a> </p>
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<p><div align="center">Figure. 9 The GUI of adding information and the image with time and scale bar</div></p>
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Software
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Almost all micrographs shown in our wiki and ppt were processed using this software. It helped us a lot and we wish to share it with anyone who needs it. If you want more detail, please refer to the user manuals. The software is available at:<a href="https://github.com/igemsoftware2018/Team_Peking">https://github.com/igemsoftware2018/Team_Peking (Github)</a>. If you want an updated version after the project freeze and after iGEM, check<a href="https://github.com/IndigoMad/Microscopic-Images-Batching"> here: (Github)</a>, we will release all the updates there.
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Latest revision as of 00:22, 18 October 2018

Software

Overview

We produce abundant fluorescence images in our experiments. However, there are many challenges in the processing of such data, which can be extremely large. Even in the case of 1 hour of imaging for 25 positions at 3 channels every minute, the microscope will yield 4500 high-resolution images. To help with the image processing in such a high throughput, we developed software for microscope image batching(Fig. 1).
(Github: https://github.com/igemsoftware2018/Team_Peking)

This software was written specifically for the problems we encountered.


Figure. 1 The GUI of the software



Naming Rules management

The first problem we met is that the file names of the exported images are generated according to fuzzy rules. Confusingly, the rules for the number of the positions, channels and times vary among files. To address the diversity of file names of images derived from different microscopes, we managed to build a naming rule manager (Fig. 2), which can create and modify the naming rule. The rules that can be made are flexible, and can contain up to 4 variables and 4 customized strings. Every variable has a customized zero filling function that can solve annoying problems such as the numbers 01 to 99. The users can also share their rules in the form of a file, which may benefit group projects. Please refer to the user manuals for more details.


Figure. 2 The GUI of naming rules manager



Grayscale and Channels Merge

After solving the problem of obtaining the files, we can now address their processing.The most important difference between fluorescence microscope images and ordinary photographs is the channel function. We needed to contrast different fluorescence channels to assess the result. However, exporting a great number of large images can be exceedingly time-consuming. Thus, if we can merge the channels or convert the images to grayscale after cropping, we will save much time. Thus, we added the functions of merging(Fig. 3) and grayscale conversion (Fig. 4)to our software first. Please refer to the user manuals for more details.



Figure. 3 The images before and after channels merging

Figure. 4 The images before and after grayscale conversion



Video and Z Stacks

In living organisms, if we want to show dynamic processes using video recordings, we will need to fuse the images in the correct order to make a video. We therefore wrote functions to export video by time or by z axis.(Fig. 5) Please refer to the user manuals for more details.




Figure. 5 The GUI of the video functions and the video exported



Cropping

In scientific research, cropping is widely used to beautify the images and emphasize the target. To meet the need for flexible cropping, we provided two cropping methods. Drawing cropping can draw the range to be cropped while position cropping crops the given position.(Fig. 6) Please refer to the user manuals for more details. Please refer to the user manuals for more details.



Figure. 6 The cropping process



Fixing Drift and Rotation

What’s more, sometime the cells float during the process of photographing, which results in the cells drifting or even rotating in the video. We will have to make a larger cropping to ensure that the cell will not move out of the field of view. To solve this problem, we wrote a function that can move the cropping frame with the cell linearly, which can fix the drifting of cells to some extent(Fig. 7). Also, we can rotate the image using the setting before cropping, by which we may also fix the rotation of the cells(Fig. 8). Please refer to the user manuals for more details. Please refer to the user manuals for more details.




Figure. 7 The videos before and after drift fixing. The yeast are less locomotive after fixing.


Figure. 8 The videos before and after rotation and drift fixing, The yeast are less rotational after fixing.



Time Scale and Scale Plate

Eventually, the micrographs in science need information attached to them before they can be shown to the public. The time scale of every frame and the scale of the cells are the most common features.(Fig. 9) We can add the time scale information to the image by the given position, start time, interval and unit. Furthermore, the scale bar, which indicates the scale of the cells, can be added by the given position, total length, length/pixel and unit. Please refer to the user manuals for more details.






Figure. 9 The GUI of adding information and the image with time and scale bar







Almost all micrographs shown in our wiki and ppt were processed using this software. It helped us a lot and we wish to share it with anyone who needs it. If you want more detail, please refer to the user manuals. The software is available at:https://github.com/igemsoftware2018/Team_Peking (Github). If you want an updated version after the project freeze and after iGEM, check here: (Github), we will release all the updates there.