Yep Lab on Jin Saeki Ko

Colony Counting using YOLOv8n

Tue, 12 May 2026 00:00:00 +0000

Model used is YOLOv8n pretrained on colonies¹, but optimized for our use. The process is as follows:

 flowchart TD
 A["Load image"] --> B["Find Petri dish with OpenCV"]
 B --> C["Create inner dish mask"]
 C --> D["Black out area outside dish"]
 D --> E["Run YOLO on masked image"]
 E --> F["Filter YOLO boxes"]
 F --> G["Count accepted colonies"]
 G --> H{"More than 300?"}
 H -->|Yes| I["Report too many to count"]
 H -->|No| J["Report final count"]
 I --> K["Draw, crop, and save output"]
 J --> K
 K --> L["Return result data"]

Flowchart outlines the steps involved in the colony counting process using YOLOv8n. Below are some sample images obtained from using the model to count colonies on our plates/public datasets. Does a pretty good job overall. We can further optimize the model (though this requires labelling of our data) and the filtering process to improve accuracy, but this is a solid starting point for our colony counting needs.

Revision to the Biofilm Assay: The Bladder Cell Invasion Protocol

Tue, 31 Mar 2026 00:00:00 +0000

Since we were having issues with the biofilm formation, as expounded upon in a previous post, Dr. Yep decided to make some revisions to the protocol. This post will be a brief overview of the changes that were propsed, and the rationale behind them.

Throughout, I’ll be referring to a paper studying decreased expression of fimbriae and its effects on the pathogenesis of CFT073¹. The paper is a good example of the bladder cell invasion protocol, and the rationale behind it.

ASM 2025

Mon, 10 Nov 2025 00:00:00 +0000

This short informal post is long overdue, but I’ll excuse myself since this website wasn’t up and running in June, when I attended the conference—and besides, I’ve been busy with other things.

I had the chance to attend ASM 2025 in LA back in June. I presented my findings along with my lab partner, and overall I’d say it was a pretty good experience.

Before this, my lab partner and I had attended a smaller research conference in January. That conference was made up mainly of undergraduates. Many disciplines from the biological sciences were represented—everything from ecology to biochemistry. Since we were all undergrads, I found it easier to walk up to posters and ask as many questions as I wanted to satisfy my curiosity, because it was mutually understood that none of us really knew much about each other’s disciplines. It was nice in this way; you could pull the “I’m ignorant just like you, help me out” card, even though any basic lack of knowledge is really my own fault.

Issues with Biofilm Formation

Mon, 27 Oct 2025 00:00:00 +0000

In the lab, Kelsey and I have been running into issues with the biofilm assay. Regardless of the incubation period, the E. coli strains that are supposed to form biofilms aren’t doing so. After a couple of failed attempts, we also tried growing Pseudomonas, which is known for robust biofilm formation, but this trial also resulted in no observable biofilm. By testing these two strains, we could assess whether the problem lies with the E. coli strains we were using or whether it stems from a systemic error in our protocol.

LB, ∆fur, and Stationary Phase

Fri, 03 Oct 2025 00:00:00 +0000

Dr. Yep noticed how ∆fur stalled earlier than the other strains. It’s not necessarily a problem, but I’d like to understand the cause. The paper should also explain this, so we’ll need the rationale anyway.

∆fur entered stationary phase early in Lysogeny Broth (LB). This didn’t happen with any of the other strains or media. Why? I’ll attempt to explain this in a few ways.

ROS Damage

Since this phenomenon was absent in all other media, I think the early stalling most likely reflects a specific interaction between the high intracellular iron characteristic of ∆fur, and some inherent property of LB.

∆waaF and Colanic Acid as a Surfactant

Sun, 21 Sep 2025 00:00:00 +0000

Over the summer, I got my hands on Escherchia coli ∆waaF. The researchers at UT Austin were kind enough to consider a collaboration. This strain overproduces colanic acid, which I wanted to take advantage of. I want to test whether external supplemementation can rescue a certain non-swarming strain. The following information will frequently reference their publication, so I will list it here¹. In the subsequent passages, I will attempt to digest their paper in a way I can understand and apply in the lab.

The Yep Lab: Iron and the Motility of CFT073

Sun, 17 Aug 2025 00:00:00 +0000

Preface

After writing a first draft of this page, which came out to a couple thousand words, I decided to break this post up into multiple posts. In this first one, I will explain only one of the several projects I’ve been working on.