Low-cost bacterial colony processing system

We worked with Dr. Parmigiani's capstone groups, and they built us a very nice device for capturing images of our plates. We now want to use it to capture images of bacterial colonies on plates and the automatically count them. We then want to export the date to an excel file with some other user inputs for processing. We were going to use a NIH built and supported program that is open source called ImageJ. There are YouTube videos online (How To Automatically Count Bacterial Colonies Using ImageJ - YouTube and Simple Method of Colony Counting using ImageJ - YouTube) demonstrating the process. You can see how manual it is. This is bad because sometimes we have 60-100 plates to count for our experiments. I just wanted to automate the process as much as possible including the data export.

Future features would be determining blue vs white colonies, and fluorescent and non-fluorescent colonies. 

Objectives


  1. Semi-automated software package for colony counting.
  2. Automated data export to Excel or csv file (including sample name, colony count, and extracted cfu calculation)
  3. Determining the number of blue and white colonies on a plate. 

Motivations


We want to enable colony counts of bacterial plates. This is a key technique in a variety of microbiology research labs and there are three ways of performing this technique. First is manually counting the colonies, which is very laborious and time consuming. Second is to purchase a commercial system (approximately $40,000-60,000), which is out of the reach of most labs that this is not a major technique. The final way is to use ImageJ, an open-source software, but this requires a lot of clicking. We want to adapt this final technique with a program that semi-automates it. If this were functional from a phone this could enable more wide-spread utility.

Qualifications


Minimum Qualifications:

Coding in Python or some other suitable language

Preferred Qualifications:

Development of GUI or UX would eb beneficial, but a desire to learn these skills is essential


Details


Project Partner:

Benjamin Philmus

NDA/IPA:

No Agreement Required

Number Groups:

1

Project Status:

Accepting Applicants

Card Image Capstone