Team:HZAU-China/Software
Software
This year, we write a series of software for our project including colony radius calculation software, mathematical model software, device demo software and the core BioPaFiAR software (driver for the BioPaFiAR hardware device). Now we will introduce them one by one.
Colony radius calculation software
In this project, the specific pattern of bacteria is formed by controlling the motility of bacteria. So the first step of this project is validating the difference of motility. In experiment, the motility can be represented by the size of bacteria colony. So we write a sequential photography program, and it can be used to take a photo every 15 minutes combined with Raspberry Pi computer. After getting these pictures, we need to measure the diameter of colony. If measured manually, it will be a huge amount of workload. So we write a Python program to help us.
It is semi-automatic software and can be used in sequential photography. When this program is running, you can see the GUI like Figure 1A; the Python shell window is also useful for you to see the measure result (Figure 1B). You need two pictures as the input to this program. The first picture is the starting point in the picture sequences and the second picture is one you want to measure.
Warning: camera and the target object cannot be moved after shooting begins and the ambient light must be Invariant.
Figure 1. Colony radius calculation software.
Procedures:
1. After running this program, click the min track bar and move the mouse. You can see that the following window will change. The white parts are colonies. Move the track bar until the colony you want to measure looks the best (clearest).
2. After the adjustment, click the left mouse button and move mouse to choose the colony you want. The selection box is a green box.
3. After choosing a colony, the area will be shown in the litter window. If there is no other colony in the window, you can press “Enter” to calculate the diameter of the colony. The result will be shown in the Python shell window. See Figure 1B.
4. Press “Esc” to quit this program.
You can click here to download this software.
Motility dynamic model software
Based on the dynamic model, we package the modeling program into a software with a GUI. The program is coded using Python 2.7 and the GUI is created using traits/traitsUI. The image processing is performed using OpenCV-python interface and the result is displayed by Mayavi. Figure 2 shows the GUI of this software.
Figure 2. Motility dynamic model software.
Procedures:
1. Run this software.
2. Click the yellow folder shape icon in the back of “Choose File” to select a target image.
3. Adjust the parameter values including k, r, ps and time.
4. Choose a display mode (2D or 3D).
5. Click “ok” button to solve PDE. The result will be shown in the bottom window. If you are interested in this program, you can download it by clicking here.
