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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
  1. Run preprocess.py to generate positive samples between spatial transcriptomics.
python prerocess.py -c ./configure/osmFISH_Zeisel.yaml
  1. Run main.py to train and predict the transcript distribution of the spatial transcriptomics.
python main.py -c ./configure/osmFISH_Zeisel.yaml

Concat

limin@mail.csu.edu.cn