Difference between revisions of "Team:Peking/Software"

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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. <a href="https://github.com/igemsoftware2018/Team_Peking">(Github: https://github.com/igemsoftware2018/Team_Peking)</a>
 
                                     <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. <a href="https://github.com/igemsoftware2018/Team_Peking">(Github: https://github.com/igemsoftware2018/Team_Peking)</a>
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<div class="texttitle">Naming Rules management
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                                     <p>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.<a href="https://static.igem.org/mediawiki/2018/3/32/T--Peking--Users_manual.pdf"> Read the user's manuals for more detail.</a>  
 
                                     <p>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.<a href="https://static.igem.org/mediawiki/2018/3/32/T--Peking--Users_manual.pdf"> Read the user's manuals for more detail.</a>  
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<div class="texttitle">Grayscale and Channels Merge
 
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                                     <p>After solving the problem of getting files, we can now stick to the practices functions practical.
 
                                     <p>After solving the problem of getting files, we can now stick to the practices functions practical.
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                                     <p>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. <a href="https://static.igem.org/mediawiki/2018/3/32/T--Peking--Users_manual.pdf"> Read the user's manuals for more detail.</a></p>
 
                                     <p>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. <a href="https://static.igem.org/mediawiki/2018/3/32/T--Peking--Users_manual.pdf"> Read the user's manuals for more detail.</a></p>
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                                     <p>In science research, cropping are widely used to beautify the images and emphasize the target. To meet the need of flexible cropping, we provide two cropping method. Drawing cropping can draw the range to be cropped while position cropping crop straightly by the given position. Read the user manuals for more detail.</p>
 
                                     <p>In science research, cropping are widely used to beautify the images and emphasize the target. To meet the need of flexible cropping, we provide two cropping method. Drawing cropping can draw the range to be cropped while position cropping crop straightly by the given position. Read the user manuals for more detail.</p>
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<div class="texttitle">Fixing Drift and Rotation
 
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                                     <p>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.<a href="https://static.igem.org/mediawiki/2018/3/32/T--Peking--Users_manual.pdf"> Read the user's manuals for more detail.</a>  </p>
 
                                     <p>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.<a href="https://static.igem.org/mediawiki/2018/3/32/T--Peking--Users_manual.pdf"> Read the user's manuals for more detail.</a>  </p>
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<p>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  <a href="https://github.com/igemsoftware2018/Team_Peking">here (Github)</a>.And if you want a update version after the project freeze after iGEM, <a href="https://github.com/IndigoMad/Microscopic-Images-Batching"> click here (Github)</a>,we will release all the update here.</p>
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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  <a href="https://github.com/igemsoftware2018/Team_Peking">here (Github)</a>.And if you want a update version after the project freeze after iGEM, <a href="https://github.com/IndigoMad/Microscopic-Images-Batching"> click here (Github)</a>,we will release all the update here.
 
                              
 
                              
 
                      
 
                      
 
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Revision as of 07:25, 16 October 2018

Home

Software

You can see our software here.

Overview

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. (Github: https://github.com/igemsoftware2018/Team_Peking)



This software is wrote just for the problems we meet.

Naming Rules management

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's manuals for more detail.



Grayscale and Channels Merge

After solving the problem of getting files, we can now stick to the practices functions practical. 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 cropping, we will save much time. Thus we add the functions of merging and grayscale to our software first. Read the user's manuals for more detail.





Video and Z Stacks

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's manuals for more detail.






Cropping

In science research, cropping are widely used to beautify the images and emphasize the target. To meet the need of flexible cropping, we provide two cropping method. Drawing cropping can draw the range to be cropped while position cropping crop straightly by the given position. Read the user manuals for more detail.





Fixing Drift and Rotation

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 cropping to ensure the cell will not go out of the edge. To solve this problem, We wrote a function that can move the cropping 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 cropping, by which we may also fix the rotation of the cells. Read the user's manuals for more detail.







Time Scale and Scale Plate

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's manuals for more detail.












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).And if you want a update version after the project freeze after iGEM, click here (Github),we will release all the update here.