SpaNN

A flexible deep neural network framework for predicting the transcript distribution of the spatial transcriptomics

Environment

• python 3.9.12
• pytorch 1.12.1
• numpy 1.21.6
• pandas 1.4.4
• scikit-learn 1.0.2

Data Available

The data used in our research can be downloaded from https://zenodo.org/record/8063157

Process

1. Unzip data and make dir for saved_model and results.

tar -zxvf data.tar.gz
mkdir result
mkdir saved_model

2. Run preprocess.py to generate positive samples between spatial transcriptomics.

python prerocess.py -c ./configure/osmFISH_Zeisel.yaml

3. Run main.py to train and predict the transcript distribution of the spatial transcriptomics.

python main.py -c ./configure/osmFISH_Zeisel.yaml

Concat

[email protected]