DeepTetrad Package

DeepTetrad: high-throughput image analysis of meiotic tetrads by deep learning in Arabidopsis thaliana

Contributions

• The project was initiated by Prof. Choi and the code is written by Dr. Lim (abysslover) at Pohang University of Science and Technology (POSTECH) Plant Genomic Recombination (PGR) Laboratory.

• This research was conducted in collaborations with the following people: Eun-Cheon Lim¹, Jaeil Kim¹, Jihye Park¹, Eun-Jung Kim¹, Juhyun Kim¹, Yeong Mi Park¹, Hyun Seob Cho¹, Dohwan Byun¹, Ian R. Henderson², Gregory P. Copenhaver³, Ildoo Hwang¹ and Kyuha Choi¹.

1. Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
2. Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
3. Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA

• The manuscript is available at bioRxiv and TPJ

Getting Started

A step-by-step tutorial is provided in the following sections.

Prerequisites

You should install CUDA-enabled GPU cards with at least 12GB GPU memory manufactured by nVidia, e.g., Titan XP.

Prepare fluorescent images

1. Take photos of pollen tetrads by using microscopy.
2. The resolution of a fluorescent image must be (2560x1920).
3. The SUFFIX of filenames is VERY IMPORTANT to be recognized by DeepTetrad. The conventions are listed below:

Filename	Description
I3bc_(1)-1.jpg	a bright-field image (first)
I3bc_(1)-2.jpg	a fluorescent image of RED light wave (second)
I3bc_(1)-3.jpg	a fluorescent image of GREEN light wave (third)
I3bc_(1)-4.jpg	a fluorescent image of BLUE light wave (fourth)

Prepare folder structures

1. Put fluorescent images into folders.
   • The parent folder name determines how DeepTetrad recognizes the name of samples. For instance, the parent folder name of I3bc (1) represents the sample name of fluorescent images.
   • The grand-parent folder name will be matched against the names in the physical T-DNA locations when determining Tetrad types. For example, "I3bc" in the figure, will be matched with "Cyan-Yellow-Red", which is the order of the protein colors of the I3bc Fluorescent Tagged Transgenic Line(FTL).

2. Prepare a T-DNA map file
   • The file is a plain text file in which FTL names with T-DNA color orders are listed.
   • An example of "T-DNA.txt" is shown below:

I1bc	GRC
I1fg	GCR
I2ab	CGR
I2fg	RGC
I3bc	CGR
I5ab	RGC

3. Examples
   • A folder structure for testing

- Fluorescent images for testing

Install DeepTetrad

1. Install Anaconda
   • Download an Anaconda distribution: Link
2. Create a Conda environment

	conda create -n pac

3. Install DeepTetrad in Linux

	conda activate pac
	conda install -c abysslover deeptetrad

4. Install DeepTetrad in Window

	conda activate pac
	conda install -c abysslover deeptetrad
	pip install deeptetrad

5. Run DeepTetrad

	conda activate pac
	deeptetrad --physical_loc=T_DNA.txt --path=./test

6. Update DeepTetrad

	conda activate pac
	conda update -c abysslover deeptetrad
	deeptetrad -r

NOTE:

1. You must activate the conda enviroment before running deeptetrad if you opened a new console.
2. The model weights are not updated by conda update command, hence you must specify -r option in the first run after the update for refreshing the model weights.

Contact

Please contact abysslover@gmail.com and kyuha@postech.ac.kr if you have any questions about DeepTetrad.