Team:TecCEM/Software

Software

Software

Index

• Introduction
• Activity Log
• Cell Count

For this year’s software, we developed a web application with three main functionalities, a cell counter, a BioBrick builder and an activity log for our hardware. Up next, we will explain each one of them!

Activity Log

The activity log is a really simple piece of software, nevertheless very important. This part of the web application is where the software and the hardware converge into a single solution. The user interface is really basic and minimalistic and shows the data obtained from the hardware as a table and as a graph.

To distinguish between all the different projects from different people we use a login. First-time users need to register into the platform which will create an account for them. Once this is done, the person can register different projects.

Figure 1. Sign up

The project signup is a bit more complex because we need a way to link the automation system (hardware) with the platform. First of all, it is necessary to have BoB, its automation system and a computer with Arduino installed on it.

Once we have this two things ready, open the arduino code called “auto.ino” - you can get the code from this repository Github Link - and set up your local wifi network as shown in Figure 2.:

Figure 2. Code configuration.

Then, we need to connect our NodeMCU board to the computer, load the program and open the serial monitor. In this monitor a token will be displayed, we need to copy and paste it in the Project Code input as shown in Figure 3

Figure 3. Adding a new project.

Once we have an account and a project set, we can visualize the data sensed from Bob. The data can be filtered depending on the date selected. The default setup shows all the data obtained throughout the projects time.

Figure 4. All data of default project.

Figure 5. All data of default project filtered by month.

The advantages of this application are the following; firstly it keeps track and displays it in form of a plot with the most relevant data of the experiments done inside BoB. For example, it could be possible to watch how is it that the color of the medium is changing and after some time relate this plots to the cell proliferation or the time it takes for some cell colonies to grow.

It also displays the CO2 and temperature which are extremely important variables of an incubator, the improvement we are seeking for our hardware.

Cell Count

The cell count software is a beta version image processing program that takes an input image and outputs a close estimate of the number of cells in the picture. The main reasons of it to still be a beta is because we would like to perform more tests on it, and once it’s done, that will return the proliferation percentage.

This software works for two kinds of cell colonies. To use it, it is necessary to access the web application and go to the section of Cell Count found on the top left hand. Upload your picture and wait for the results.

Figure 6. Cell Selection Cell Count

Figure 7. Result Test 1 Cell Count

Figure 8. Result Test 2 Cell Count

This software is planned to be a relief for a lot of researchers that make this process the hard way. This will optimize time, effort and resources letting the scientists do more science and less counting.

Figure 9. Image to be processed Cell Count

Figure 10. Image processeed by our software

Figure 11. Approximation of cell count

In this example, we got an approximation of 990 cells counted.

Figure 11. Second result

Figure 12. Second numeric approximation