Team:XMU-China/Content4

We used Matlab to help us solve the four DDEs and draw the graphs. In addition, we developed a GUI user interface after finishing the main DDE code. The user interface makes people easier to modify and adjust the parameters without recoding the .m files and any Matlab language knowledge. We called this software “Gene oscillate simulator”.

“Gene oscillate simulator” has two main modes of simulations. The basic simulation is designed for the oscillate circuit with LuxI, aiiA and LuxR, while the advanced simulation adds the effect of ndh gene. In each of the modes, users can make a series of graphs though designing the different parameters. The numbers of graphs mainly depend on the different parameters and the modes.

The meaning of each parameter can be displayed when click each parameter or right click each input box. For the people first use this software, we designed the “one example” function which can set the parameters suitably in a single time.
To get an idea about the different conditions in which oscillations could occur, we created a function which allows users to enter the range in which the variables should be varied and compare their results in the results. Due to the arithmetic speed, we finally apply this function in fluid flow speed and cell density, which are the most important parameters in the model. For example, people can set the cell density range from 0.1 to 0.9 with the step 0.2 by not selecting the ’Fix the cell density’ item.
A white noise system was coded to simulate the noisy environment in the medium. This function makes the model closer to the actual environment. Users can set the strength by clicking “add white noise” box and inputting the decibels.
A script calculates amplify and period of the oscillation is also added as an additional function. This allows our software detect and compare the characteristic of certain oscillation.
After setting all the parameters, users can save and output these settings into a standard 2003 excel file through the file menu. Loading is also supported which makes more convince for transmitting the parameters.
Before draw the graphs users need to choose the plot mode when range parameters exist. For example, when set the cell density the software will ask user to draw separately or put curves with different cell density together.

Then clicking the “draw” button, the software iterates over the values and plots graphs of all combinations possible for that range of values. After calculating, at most 3 kinds of graphs can be given, (1) concentration alteration of four main protein (2) fluorescence alteration under different cell density and fluid flow speed (3) amplify and period alteration under different cell density and fluid flow speed.

To protect the software and computer, we designed an error-stop system which could stop the simulation as soon as one error was detected. This system also is called when users click “cancel” button to stop the calculation. But different with error happened; this stop process takes about 1 min. The arithmetic speed of this software depends on the complexity of the parameters. Choosing both cell density range and fluid flow range to calculate can sometimes take more than 10 minutes. It is mainly because the large numbers of nested for-loops in the script and the slowly calculate speed about Matlab core.

做微流体实验中,我们多次连续8小时左右通过荧光显微镜拍到了大量的照片.但是更大的工作量是处理照片得到我们想要的数据.之前我们使用的软件只能进行手动处理,并且最大的瓶颈在于不能批量处理照片.因此我们使用MATLAB编码了自己的新程序,批量处理实验照片得到数据,大大节约了我们的时间.

原理

ImageMe的主要算法是先将读入的照片进行灰度化处理,之后进行边缘处理从而得到照片中图形的边缘,接着寻找每个格子的边界,最后对每个格子的灰度进行积分.