This repo contains all the code used in Bi et al.(2023).

This repository includes:

1. Quick sample code.
2. Thresholding methods
   • 2.1 Single threshold method.
   • 2.2 Adaptive threshold method.
3. Mask RCNN method
   • 3.1 LabelMe.
   • 3.2 Mask-RCNN method
     • 3.2.1 Training Mask-RCNN model
     • 3.2.2 Predict depth images by trained Mask-RCNN model.
4. Build Body Weight Regression Model
   • 4.1 Data Preprocessing
   • 4.2 Goodness of fit
   • 4.3 Cross-Validation 1
   • 4.4 Cross-Validation 2

Attention: This sample code works with example images. For your customized images, many hyperparameters need to be adjusted.

• Download python folder from this github into your local postion.
• Install all the packages you will use in requirement.txt. Recreate one conda environment follow the lines.

# $ conda create --name <env> --file <requirement.txt>

• Build one empty folder named outputs within your local folder python which you downloaded from this github repository.
• If you want to run for your own figures, please make sure your files following our Sample_files folder structure.

• Please make sure the outputs folder is empty before running each image analysis method.

Select one image analysis method below and run the related code block

• Single threshold method:

python single_thr/ImageAnalysis_single_thr.py D1

• Adaptive threshold method:

python adaptive_thr/ImageAnalysis_adaptive_thr.py D1

• Mask R-CNN method:

python maskrcnn/ImageAnalysis_mrcnn.py D1

After running, each approach will generate one csv file in outputs/D1folder similar to the following.

• .py file

• .py file

• The code was forked from https://github.com/uf-aiaos/ShinyAnimalCV
• How to install LabelMe
• How to use LabelMe to label image

## How to used our customized LabelMe.
## Code used to start label png into json files.
labelme ./depth/cow.png -O ./outputs/cow.json

# Code used to transfer json files into folders.
labelme_json_to_dataset ./outputs/cow.json -o ./outputs/cow_json

• The code was forked from https://github.com/uf-aiaos/ShinyAnimalCV
• .ipynb file
• .h5 file

• .py file

• .Rmd file

• .Rmd file

• .Rmd file

• .Rmd file