Difference between revisions of "Team:Peking/Software"

 
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         <meta name="description" content="Wiki of Peking iGEM 2018" />
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         <meta name="author" content="Li Jiamian & Wang Yuqing"/>
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                                 </ul>
 
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                             </li>
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                             <li class="dropdown menu-3"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Modeling</a>
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                             <li class="menu-3"><a class="colapse-menu1" href="https://2018.igem.org/Team:Peking/Model">Modeling</a>
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                                <ul class="dropdown-menu">
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                                    <li><a href="https://2018.igem.org/Team:Peking/Modeling_overview">Overview</a></li>
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                                    <li><a href="https://2018.igem.org/Team:Peking/SPOT_Formation" class="barfont1">SPOT Formation</a></li>
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                                    <li><a href="https://2018.igem.org/Team:Peking/Application" class="barfont1">Application</a></li>
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                                </ul>
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                             </li>
 
                             </li>
 
                             <li class="menu-4"><a class="colapse-menu1" href="https://2018.igem.org/Team:Peking/Software">Software</a>
 
                             <li class="menu-4"><a class="colapse-menu1" href="https://2018.igem.org/Team:Peking/Software">Software</a>
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                                <li class="dropdown menu-6"><a class="dropdown-toggle" data-toggle="dropdown" href="#">Human Practices</a>
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                            <li class="menu-6"><a class="colapse-menu1" href="https://2018.igem.org/Team:Peking/Human_Practices">Human Practices</a>
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                                    <ul class="dropdown-menu">
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                            </li>
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                                        <li><a href="https://2018.igem.org/Team:Peking/Human_Practices" class="barfont1">Overview</a></li>
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                                        <li><a href="https://2018.igem.org/Team:Peking/Statistics" class="barfont1">Statistics</a></li>
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                                        <li><a href="https://2018.igem.org/Team:Peking/Public_Engagement" class="barfont1">Public Engagement</a></li>
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                                        <li><a href="https://2018.igem.org/Team:Peking/Other" class="barfont1">Other</a></li>
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                                </li>
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                                 <li class="dropdown menu-7"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Achievement</a>
 
                                 <li class="dropdown menu-7"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Achievement</a>
 
                                     <ul class="dropdown-menu">
 
                                     <ul class="dropdown-menu">
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                                         <li><a href="https://2018.igem.org/Team:Peking/Collaborations" class="barfont1">Collaborations</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/Safety" class="barfont1">Safety</a></li>
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                                        <li><a href="https://2018.igem.org/Team:Peking/Acknowledgement" class="barfont1">Acknowledgement</a></li>
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                                     </ul>
 
                                     </ul>
 
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                     <h1>Software </h1>
 
                     <h1>Software </h1>
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                     <p class="title1" style="text-align:center;">You can see our software here.</p>
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                                    <h4><a href="javascript:void(0);" onclick="naver('A')">&bull;Overview</a></h4>
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                                    <h4><a href="javascript:void(0);" onclick="naver('B')">&bull;Naming&nbsp;Rules&nbsp;Management</a></h4>
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                                    <h4><a href="javascript:void(0);" onclick="naver('C')">&bull;Grayscale&nbsp;&&nbsp;Merge</a></h4>
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                                    <h4><a href="javascript:void(0);" onclick="naver('D')">&bull;Video&nbsp;&&nbsp;Z&nbsp;Stacks</a></h4>
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                                    <h4><a href="javascript:void(0);" onclick="naver('E')">&bull;Cropping</a></h4>
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                                    <h4><a href="javascript:void(0);" onclick="naver('F')"> &bull;Fixing&nbsp;Drift&nbsp;&&nbsp;Rotation</a></h4>
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                                    <h4><a href="javascript:void(0);" onclick="naver('G')">
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                                  &bull;Time&nbsp;Scale&nbsp;&&nbsp;Scale&nbsp;Plate</a></h4>
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                            <div class="texttitle"> Software
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<div class="texttitle"> Overview
 
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                                <div class="content">
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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).
 +
<br/><a href="https://github.com/igemsoftware2018/Team_Peking">(Github: https://github.com/igemsoftware2018/Team_Peking)</a><br/>
 +
<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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<div align="center">
 +
<img src="https://static.igem.org/mediawiki/2018/5/52/T--Peking--Software.png" width="300 px" height="300 px"></div>
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<p><div align="center">Figure. 1 The GUI of the software</div></p>
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<br/><br/>
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<div class="coll">                         
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<div class="texttitle">Naming Rules management
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<a id="B"></a></div>
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    <hr style="border:2px dashed; height:2px" color="#666666">
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                                <div class="content">
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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>
 +
<br/><br/>
 +
<div align="center">
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<img src="https://static.igem.org/mediawiki/2018/d/dd/T--Peking--Namerule.png"><br/>
 +
<p><div align="center">Figure. 2 The GUI of naming rules manager</div></p>
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<br/><br/>
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</div>
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<div class="coll">
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<div class="texttitle">Grayscale and Channels Merge
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<a id="C"></a></div>
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                                <div class="content">
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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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<br/><br/>
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<div align="center">
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<img src="https://static.igem.org/mediawiki/2018/e/ee/T--Peking--MergeG.png" width="150 px" heigth="150 px">
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<img src="https://static.igem.org/mediawiki/2018/e/ef/T--Peking--MergeR.png" width="150 px" heigth="150 px">
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<img src="https://static.igem.org/mediawiki/2018/2/27/T--Peking--MergeM.png" width="150 px" heigth="150 px">
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</div>
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<p><div align="center">Figure. 3 The images before and after channels merging</div></p>
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<div align="center">
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<img src="https://static.igem.org/mediawiki/2018/e/eb/T--Peking--GrayS.png" width="150 px" heigth="150 px">
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<img src="https://static.igem.org/mediawiki/2018/4/49/T--Peking--GrayG.png"width="150 px" heigth="150 px">
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</div>
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<p><div align="center">Figure. 4 The images before and after grayscale conversion</div></p>
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<br/><br/>
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</div>
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</div>
 
                             <div class="coll">
 
                             <div class="coll">
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<div class="texttitle">Video and Z Stacks
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<a id="D"></a></div>
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                                 <div class="content">
 
                                 <div class="content">
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                                     <p>We produce abundant fluorescent images in our experiments. However, there are many troubles when taking into the processing those data. The data can be extremely large. Even if you just take a 1 hour imaging for 25 positions in 3 channel for every minutes, the microscope will yield 4500 high resolution images. To help with the image processing in such a high throughput, we developed a software aim at microscope images batching.
+
                                     <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>
 
<br/><br/>
 
<br/><br/>
−
This software is wrote just for the problems we meet.  
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<div align="center">
 +
<img src="https://static.igem.org/mediawiki/2018/7/77/T--Peking--video.png"><br/>
 +
<img src="https://static.igem.org/mediawiki/2018/0/09/T--Peking--driftE.gif"></div>
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<p><div align="center">Figure. 5 The GUI of the video functions and the video exported</div></p>
 
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The first problem we meet is the file name of the exported images are always in massy rules. What’s the most confusing, the rules of number of the positions, channels and time are various in files. Considering the diversity of file names of images derived from different microscopes, we manage to build a naming rule manager, which can create and modify the name rule. The rules can be made are flexible, which can contain up to 4 variables and 4 customized string. Every variables have a customized zero filling function that can solve the problem like the annoying number 01 to 99. The users can also shear their rules in the form of a file, which may benefit group working. Read the user manuals for more detail.
+
 
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</div>
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</div>
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                            <div class="coll">
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<div class="texttitle">Cropping
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<a id="E"></a></div>
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                                <div class="content">
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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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<br/><br/>
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After solving the problem of getting files, we can now stick to the practices functions practical.
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<div align="center">
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<img src="https://static.igem.org/mediawiki/2018/9/96/T--Peking--cropping.png" width="600px" height="300 px"></div>
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<p><div align="center">Figure. 6 The cropping process</div></p>
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The most important difference between fluorescent images of microscope and Ordinary photo is the function of channel. We need to contrast different fluorescent channel to discover the conclusion. However, export a large number of large images could be a time-wasting process. If we can merge channel or convert the images into grayscale after chopcropping, we will save much time. Thus we add the functions of merging and grayscale to our software first. Read the user manuals for more detail.(此处放处理前后的图)
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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>
 
<br/><br/>
 
<br/><br/>
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For the living organism, if we want to show the dynamic process with video, we will need to fuse the images by order to make video. We wrote the functions to export video by time or by z axis. Read the user manuals for more detail.（此处放导出的视频gif）
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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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<br/><br/>
 
<br/><br/>
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In science research, chopcropping are widely used to beautify the images and emphasize the target. To meet the need of flexible chopcropping, we provide two chopcropping method. Drawing chopcropping can draw the range to be chopcropped while position chopcropping chopcrop straightly by the given position. Read the user manuals for more detail. (此处放软件使用截图)
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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>
 
<br/><br/>
 
<br/><br/>
−
What’s more, sometime the cells float in the process of photographing, which result in the cell drift or even rotate in the video. We will have to make a larger chopcropping to ensure the cell will not go out of the edge. To solve this problem, We wrote a function that can move the chopcropping frame with the cell linearly, which can fix the drift of cell to some extent. Also, we can rotate the image by the setting before chopcropping, by which we may also fix the rotation of the cells. Read the user manuals for more detail. (漂移校正前后对比动图，旋转漂移校正前后对比动图)
+
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<br/><br/>
 
<br/><br/>
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Eventually, the microscopy images in science need some information on it before showing up in public. The time scale of every frame and the scale of the cell are the most common features. We can add the time scale information to the image by the given position, start time, interval and unit. And the scale plate, which indicate the scale of the cells, can be added by the given position, total length, length/pixel and unit. Read the user manuals for more detail. (加标尺和时间的动图)
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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>
 
<br/><br/>
 
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Almost all of the microscopy image shown in our wiki and ppt are processing with this software. It help us a lot and we wish to share it with anyone who need it. If you want more detail, read the user manuals and the software are available here. (Github链接) And if you want a update version after the project freeze after iGEM, check here (另一个Github链接)， we will release all the update here.
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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.