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Revision as of 15:03, 17 October 2018

Cell Gif

Software

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.

signup activity-log
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.:

configuration activity-log
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

Adding Project activity-log
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.

Default data activity-log
Figure 4. Default data config. vs. Data filtered by month

The advantages of this application are the following:

  • It keeps track and displays the most relevant data from the experiments in form of a plot. 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 can be accessed from anywhere in the world

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 return the confluence percentage, as well as perform more tests on the software.

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.

cell selection cellcount
Figure 6. Cell Selection Cell Count
result 1 cellcount
Figure 7. Result Test 1 Cell Count
result 2 cellcount
Figure 8. Result Test 2 Cell Count
process cellcount
Figure 9. Image to be processed Cell Count
result after cellcount
Figure 10. Image processeed by our software
numeric approximation result after cellcount
Figure 11. Approximation of cell count

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

second test result after cellcount
Figure 11. Second result
second numeric approximation result after cellcount
Figure 12. Second numeric approximation

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.