Brief Overview

This post documents a bioinformatics workflow for the algal species Codium fragile, also known colloquially as “Dead Man’s Fingers” due to its finger-like morphology. This workflow demonstrates the process of identification and phylogenetic analysis through the use of the NCBI website, NCBI primer BLAST, and MEGA software with the gene tufA as the target gene. The tufA gene was selected since it is widely considered as a robust barcode for green macroalgae, providing highly distinct interspecific variations and ability to detect cryptic species.

Overall Structure

Each tank system has three aquariums with a singular sump system filtering the water for all three. As such, each triplicate system is in reality one tank, which should be considered when designing an experiment. The systems are numbered clockwise from 1-12, with tanks 1-6 being on the left, and 7-12 on the right.

Summary of Findings

• The best color consistency (lowest variation) was achieved by applying the custom white balance based on the 24% white patch to ambient images (Figure 3) and analyzing the chromaticity of the colors rather than raw brightness levels.
• The strobe lit images also had a great consistency (Figure 4).
• Using chromaticity instead of raw brightness levels appears to be an effective method of analyzing the colors across images even under different lighting conditions.

Purpose:

Become familiarized with established scientific chlorophyll measurement methods via homogenization of tissue and subsequent optical density wavelength readings. This data serve as the ground truth data to compare the chlorophyll measuremnts garnered from imaging based RGB pixel data.

Purpose:

The goal of this training was to provide me with the tools to build a pipeline to collect chlorophyll from image data. On this dive, we took images of Oculina off the coast of Sdot Yam. Once the images were collected, we also collected physical samples. The goal is to build an image processing pipeline that has the same results as lab chlorophyll processing techniques.

Purpose:

This protocol provides a step-by-step guide for setting up and using Git on a Mac to connect to GitHub using SSH. It is designed for lab members who need to track and share their research code, analysis, and documentation on GitHub without relying on the GitHub Desktop application. With this method, you can communicate with Github via Mac’s terminal.

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