PhenoLearn

PhenoLearn is an open-source image analysis tool that is designed for high-throughput phenotype measuring on digital biodiversity datasets. It can (i) generates annotations (ii) use deep learning models to generate annotations (iii) Review predictions.

Update (2025/05/18)

Publication Announcement

Our paper introducing PhenoLearn has been published in the Journal of Evolutionary Biology!
"PhenoLearn: A user-friendly toolkit for image annotation and deep learning-based phenotyping of biological datasets"

Read the paper here

Video Tutorial

A short 2-minute video tutorial for PhenoLabel (the annotation component of PhenoLearn) is available:
Watch the tutorial here

Latest Windows Executable

The latest Windows .exe (built on 2025/05/18) can be found in the latest release

Major Features updates:

• Support for exporting segmentation masks with multiple segmentation classes

• Customizable brush size

Table of Contents

• Features
• Installation
• Get demo datasets
• Usage
• License
• Contact

Features

PhenoLearn has two UI tools:

1. PhenoLabel. does the Label and Review
2. PhenoTrain. does the Deep Learning

Functions:

• Labeling: Place labels on images, currently supports points and segmentations.
• Using Deep Learning: Train DL models with labelled images, and apply the best model to make predictions.
• Review: Review the predictions, edit incorrect predictions to increase the accuracy

PhenoLearn can be used in different workflows

Installation

Before you start the installation, make sure your system meets the following requirements:

• Python 3 (Tested Versions: 3.11) installed. If you don't have Python installed, you can get it from Python or Anaconda Python. We recommend Anaconda Python, as it has Conda included.
• pip (Python Package Installer), which typically comes with the Python installation
• Conda, an open-source package management system and environment management system

To install, follow these steps.

1. Clone the repo

git clone https://github.com/EchanHe/PhenoLearn.git

It is recommended to create a virtual environment to avoid mixing up the project dependencies with other projects. You can create a virtual environment using the following command:

2. Create a new Conda environment and activate it:

The python version we developed PhenoLearn is 3.10.

conda create --name phenolearn python=3.10 
conda activate phenolearn

You can also custom your environment. For further information about virtual environment you can visit here

3. Install pacakges:

When you are in the phenolearn virtual environment, install packages for PhenoLearn.

Required packages for PhenoLabel with tested versions:

• numpy == 1.25.1
• pandas == 2.0.3
• opencv-python == 4.8.0.74
• PyQt == 5.15.9
• TensorBoard == 2.13.0

Other versions may also work, but they have not been tested.
Use the requirements.txt in the root directory to install

pip install -r requirements.txt

You can also install these packages directly using pip:

pip install numpy==1.25.1 pandas==2.0.3 opencv-python==4.8.0.74 PyQt5==5.15.9 TensorBoard == 2.13.0

We used PyTorch, a deep learning library, to implement PhenoLearn.

The initial version was 2.0.1, and we have also tested our work on 2.2.2, which was the latest stable version as of 2024/04/02.

To install PyTorch, it depends on whether your device has a CUDA-supported GPU. You must install the correct version of PyTorch accordingly. For detailed installation instructions, please visit the official website. For installing previous versions, visit here.

Note: This error could occur when trying to run PhenoLearn

QObject::moveToThread: Current thread (<Thread_id>) is not the object's thread (<Thread_id>).

Cannot move to target thread (<Thread_id>)

qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in <path_to_your_environment>/site-packages/cv2/qt/plugins even though it was found.

This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

This error often happens in Linux. Visit here for detailed information about this error.

To solve this, uninstall opencv-python and install opencv-python-headless

pip uninstall opencv-python
pip install opencv-python-headless

4. Run PhenoLearn

PhenoLabel

Navigate to the repository in the terminal and run

python phenolabel.py

Or open the repo using Visual studio Code The run the phenolabel.py file

Or for Windows users, a binary version of PhenoLabel (e.g., an .exe file) is available at https://zenodo.org/records/10909841.

PhenoLearn provides an intuitive interface to easily label images for Deep Learning purposes.
The window when PhenoLabel starts

PhenoTrain

Navigate to the repository in the terminal and run

python phenotrain.py

Or open the repo using Visual studio Code The run the phenotrain.py file
PhenoTrain provides an intuitive interface for using Deep Learning.
The window when PhenoTrain starts

PhenoTrain also provides a command line interface to train models.
Use python phenotrain_cli.py --help to see the available options. For example,

python phenotrain_cli.py train --mode Segmentation --format CSV --csv ./data/demo/seg.csv --img-dir ./data/demo/bird_10 --scale 100 --lr 0.001 --batch 1 --epochs 10 --test-percent 20 --train-level 1

Get demo datasets

1. 10 Bird images

This dataset is designed for testing PhenoLearn:

Location: ./data/demo/

• The bird_10 folder has 10 images. They can be used for labeling and training purposes.
• bird_10_process.json is a saved labeling process file that can be loaded into PhenoLabel.
• pts.csv is a point CSV file. It stores image names in bird_10/ with three points on them. It can be used in PhenoTrain training
• seg.csv is a segmentation CSV file. It stores image names in bird_10/ with one segmentation. It can be used in PhenoTrain training
• The valid_10 folder has 10 images. They can be used for PhenoTrain prediction.
• valid_10_name.csv provides the filenames for each image in valid_10/, useful for PhenoTrain predictions.
• valid_10_props.csv is a demo property file with properties for each image in valid_10/, which can be imported into PhenoLabel.

2. The 220 bird images used in the paper

120 images are in the train folder
100 images are in the pred folder
The segmentation CSV is seg_train.csv The name file for prediction images is name_file_pred.csv

3. The 220 Littorina images

120 images are in the train folder
100 images are in the pred folder
The Point CSV file is pts_train.csv The name file for prediction images is name_file_pred.csv

Both dataset 2 and 3 can be download here: https://zenodo.org/records/10988826

Usage

• Label Image
• Use Deep Learning
• Review Predictions

Label Image

This part uses PhenoLabel

• Open a project
• Placing points
• Placing segmentations
• Fast Labelling
• Saving and Loading Labeling Progress
• Export labels

Open a project

Click on the Open Dir in the File menu to select a directory containing the images to be labeled.

After selecting the directory, PhenoLearn will display all the images in the selected folder in the File panel

Click on an image to display it in the Main panel. Here, you can inspect the image and zoom in or out using functions in View menu, or use Ctrl mouse wheels. The coordinates and RGB value of the current mouse location are displayed in bottom right

Placing points

Activate the Point button in the Toolbar.

Left-click on the image in the Main panel to place a point. A pop-up dialog will appear, allowing you to name the point. You can either enter a new name or select an used name from the dropdown menu.

You can view, edit, and delete existing points in the Annotation panel.

Placing segmentations

Toggle the Segmentation button in the Toolbar. A Segmentation Toolbar will appear below the main toolbar.

Define segmentation classes by selecting the Segmentation tab in the Annotation panel and clicking the Add button.

To segment an image, select a segmentation class and activate the Draw button in the Segmentation Toolbar. Left-click and hold to segment, which will be colored based on the color assigned.

For larger regions, draw a closed outline and click Auto Fill in the Segmentation Toolbar to fill the area inside the outline.

Activate the Erase button and erase over the incorrectly segmented area.

Fast Labelling

If you often place the same labels across multiple images, PhenoLearn's Fast Labelling feature can help speed up the process.

Click Fast Labelling in the Toolbar. It uses the annotations from the current image as pre-defined annotations for subsequent images. (Note that labels must be placed in the same order to ensure accuracy).

Saving and Loading Labeling Progress

You can save your progress at any point by selecting Save or Save As from the File menu. The progress will be saved as a JSON file.

To continue a previous session, use Open Labelling Progress from the File menu to load a previously saved file.

Export labels

Labels from PhenoLearn can be exported via export functions in File menu and used as input for Deep Learning models.

PhenoLearn supports exporting annotations in CSV files (both point and segmentation) and black and white masks (only for single-class segmentation).

Use Deep Learning

This part uses PhenoTrain

• Model Training
• Model Prediction

Model Training

In the Train tab. There are settings you need to define here:

Setting	Description
Model Type	Point or Segmentation Mask R-CNN for point DeepLab for segmentation.
Input Format	The default option is CSV. The option Mask is available when the model type is set to single-class segmentation.
Annotation File	Annotation file exported from PhenoLearn.
Image Folder	The folder of the images.
Folder of Black and White Masks	The folder of the masks when Input Format is Mask
Image Resize Percentage	The percentage of resizing the original image Range 1-100%
Validation Set Percentage	Indicates the percentage of images used in the validation. Default 80/20
Batch Size	The batch size for one iteration of training.
Training Epochs	Training length One epoch is defined as one pass of the full training set
Learning Rate	Determines how quickly or slowly a neural network model learns a problem.
Training Level	Both DeepLab and Mask R-CNN use pre-trained parameters. It shows portion of a model is trained on your dataset. Options are Minimal, Intermediate, and Full.
CPU/GPU	Select whether to use the CPU or GPU for training. If GPU is selected but no GPU is available on the device, the training will automatically default to the CPU.

Click Train to start training. Once completed, a .pth file will be saved in the saved_model folder of the PhenoLearnDL root directory.

The training logs can be viewed in TensorBoard. They are saved in the runs folder. Run the command.

tensorboard --logdir runs

Then visit http://localhost:6006/ in your browser to view the logs. For detail, you can visit the tutorial of TensorBoard.

Model Prediction

In the Predict tab. There are settings you need to define here:

Setting	Description
Model Type	Point or Segmentation
Output Format	Choose either a PhenoLearn compatible CSV file or black and white masks (only for Segmentation).
Model File	This should be a .pth file saved in training.
Prediction File Folder	The directory where the prediction file will be saved.
Image Folder	The directory containing the images for which predictions are to be made.
Name File	A CSV file with a column 'file' for image names. The name file can be generated by exporting a CSV file PhenoLearn when no annotations are placed.
Image Resize Percentage	The percentage of resizing the original image Range 1-100% This should be the same value used in training.
CPU/GPU	Select whether to use the CPU or GPU for predicting. If GPU is selected but no GPU is available on the device, the predicting will automatically default to the CPU.

Click Predict to start predicting. Once completed, prediction will be saved in Prediction File Folder.

Review Predictions

This part uses PhenoLabel

• Import Predictions
• Review Mode
• Review Assistant

Import Predictions

1. Open an image folder in PhenoLearn, just like in Image Labeling.
2. Import your model's predictions into PhenoLearn using the import functions in File menu. PhenoLearn can import CSV files and black-and-white masks.
3. After importing, PhenoLearn will visualize the predictions for reviewing

Review Mode

The Review Mode allows users to quickly skim through predictions and flag any inaccuracies.

Activate the Review Mode in Toolbar. PhenoLearn will display multiple thumbnails of images along with their annotations.

As you skim through the results, tick the checkboxes next to the thumbnails of images with incorrect predictions.

After you've reviewed the images, click the Show Flagged Images button to display only the images you flagged.

Toggle Show Flagged Images in Toolbar to only filter the flagged images. And un-toggle Review Mode to edit them

Review Assistant

The Review Assistant allows you to sort and filter images based on their properties.
Import properties using the Import Properties in File menu.

• Numerical properties can be used for sorting
• Categorical properties can be used for filtering

Known Issues and Troubleshooting

1. PyQt5 Installation on macOS

• Issue: Installing PyQt5 could happen on a macOS system may fail.
• Solution:
  1. Install PyQt5 using Homebrew:

     brew install pyqt

  2. Add PyQt5 to your PYTHONPATH in your IDE (e.g., PyCharm).
  3. Reference Stack Overflow thread for more details.

2. SSL Certificate Error

• Issue: The error urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED]> could occur when starting training with PhenoTrain on macOS.
• Solution:
  1. Navigate to /Applications/Python 3.x (replace x with your Python version, e.g., Python 3.10).
  2. Double-click Install Certificates.command to install the SSL certificates.
  3. Restart your Python environment or IDE and try again.

License

MIT