Tutorials

This section contains various short examples showcasing core Bering functionality.

Object

This section contains the introduction of Bering object

• Understand Bering object

Graph

This section contains the definition of Bering graph and data container for deep learning

• Understand Neighbor Gene Component and Co-localization Graphs

Training

This section contains the training procedure of Bering (Image-free and image-dependent modes)

• Train Node Classification Model without Graph
• Convolutional Neural Network hyperparameters for image embeddings
• Graph Convolutional Network Structure
• Image-free segmentation vs. Image-dependent segmentation
• RBF Kernel hyperparameters

Plotting

This section contains the plotting of the segmentation results

• Visualize Cell Segmentation Performance
• Visualize background noise and cell type classification
• Visualize input data of different spatial technologies
• Visualize Single Cell Data Using Segmentation Results
• Visualize Model Prediction of whole slices

Transfer learning

This section contains the pretrained models and transfer learning + self-distillation strategty

• Available pretrain models
• Visualize Model Prediction of whole slices
• Transfer pretrained model to predict tumor microenvironment