a pipeline to process brain connectivity and spatial transcriptomics for integrative analysis
pip install BrainConnectconda create -n neuron python=3.12
conda activate neuron
pip install BrainConnectBrainConnect [-h] [-v] <command> ...BrainConnect - Complete neuronal data analysis workflow
options: -h, --help show this help message and exit -v, --version show program's version number and exit Workflow commands: <command> download Download Allen experimental data preprocess Preprocess experimental data swc SWC file processing and analysis feature Feature extraction and integration fusion Multimodal data fusion model Model training and prediction
Complete workflow examples:
# 1. Download experimental data
BrainConnect download --experiments data/experiments.csv --download-dir data/experiment_data --annotation data/annotation_25.nrrd --limit 10
# 2. Preprocess experimental data
BrainConnect preprocess --experiments data/experiments.csv --download-dir data/experiment_data --annotation data/annotation_25.nrrd --output-dir data/experiment_data/result
# 3. Process SWC files
BrainConnect swc --annotation data/annotation_25.nrrd --input data/orig_swc_data/ --output results/swc_results.csv
# 4. Extract features
BrainConnect feature --swc-results results/swc_results.csv --adjacency data/Mouse_brain_adjacency_matrix.csv --output results/features.csv
# 5. Data fusion
BrainConnect fusion --features results/features.csv --experiment-results data/experiment_data/result/merged_results.csv --output results/fusion_results.csv
# 6. Train model
BrainConnect model --fusion-results results/fusion_results.csv --gene-data data/gene_data.csv --output results/gene_importance.csvRequirements:
- Python 3.12+
- Dependencies: pandas, numpy, tensorflow, pyswcloader, networkx
Version: 1.0.0
Download Experimental Data:
BrainConnect download [-h] --experiments EXPERIMENTS --download-dir DOWNLOAD_DIR --annotation ANNOTATION [--allen-tree ALLEN_TREE] [--acro-dict ACRO_DICT] [--limit LIMIT]
options: -h, --help show this help message and exit --experiments EXPERIMENTS, -e EXPERIMENTS Experimental data file path --download-dir DOWNLOAD_DIR Data download directory --annotation ANNOTATION, -a ANNOTATION Brain annotation file path --allen-tree ALLEN_TREE Allen brain tree file path --acro-dict ACRO_DICT Acronym dictionary file path --limit LIMIT, -n LIMIT Download quantity limit (0 means download all)
Example:
BrainConnect download \ --experiments data/experiments.csv \ --download-dir data/experiment_data \ --annotation data/annotation_25.nrrd \ --limit 10
Preprocess Experimental Data:
BrainConnect preprocess [-h] --experiments EXPERIMENTS --download-dir DOWNLOAD_DIR --annotation ANNOTATION --output-dir OUTPUT_DIR [--allen-tree ALLEN_TREE] [--acro-dict ACRO_DICT] [--use-projection-density]
options: -h, --help show this help message and exit --experiments EXPERIMENTS, -e EXPERIMENTS Experimental data file path --download-dir DOWNLOAD_DIR Data download directory --annotation ANNOTATION, -a ANNOTATION Brain annotation file path --output-dir OUTPUT_DIR Preprocessing results output directory --allen-tree ALLEN_TREE Allen brain tree file path --acro-dict ACRO_DICT Acronym dictionary file path --use-projection-density Use projection density data
Example:
BrainConnect preprocess \ --experiments data/experiments.csv \ --download-dir data/experiment_data \ --annotation data/annotation_25.nrrd \ --output-dir data/experiment_data/result
Process SWC Files:
BrainConnect swc [-h] --annotation ANNOTATION --input INPUT --output OUTPUT [--resolution RESOLUTION] [--allen-tree ALLEN_TREE] [--acro-dict ACRO_DICT]
options: -h, --help show this help message and exit --annotation ANNOTATION, -a ANNOTATION Brain annotation file path --input INPUT, -i INPUT Input SWC file directory path --output OUTPUT, -o OUTPUT Output results file path --resolution RESOLUTION, -r RESOLUTION Resolution parameter --allen-tree ALLEN_TREE Allen brain tree file path --acro-dict ACRO_DICT Acronym dictionary file path
Example:
BrainConnect swc \ --annotation data/annotation_25.nrrd \ --input data/orig_swc_data/ \ --output results/swc_results.csv \ --resolution 25
Extract Features:
BrainConnect feature [-h] --swc-results SWC_RESULTS --adjacency ADJACENCY --output OUTPUT [--allen-tree ALLEN_TREE] [--acro-dict ACRO_DICT] [--progress-file PROGRESS_FILE]
options: -h, --help show this help message and exit --swc-results SWC_RESULTS, -s SWC_RESULTS SWC processing results file path --adjacency ADJACENCY, -adj ADJACENCY Adjacency matrix file path --output OUTPUT, -o OUTPUT Output features file path --allen-tree ALLEN_TREE Allen brain tree file path --acro-dict ACRO_DICT Acronym dictionary file path --progress-file PROGRESS_FILE Progress save file path
Example:
BrainConnect feature \ --swc-results results/swc_results.csv \ --adjacency data/Mouse_brain_adjacency_matrix.csv \ --output results/features.csv
Data Fusion:
BrainConnect fusion [-h] --features FEATURES --experiment-results EXPERIMENT_RESULTS --output OUTPUT [--adjacency ADJACENCY] [--allen-tree ALLEN_TREE] [--acro-dict ACRO_DICT] [--min-path-length MIN_PATH_LENGTH]
options: -h, --help show this help message and exit --features FEATURES, -f FEATURES Features file path --experiment-results EXPERIMENT_RESULTS, -er EXPERIMENT_RESULTS Experimental data results file path --output OUTPUT, -o OUTPUT Output fusion results file path --adjacency ADJACENCY Adjacency matrix file path --allen-tree ALLEN_TREE Allen brain tree file path --acro-dict ACRO_DICT Acronym dictionary file path --min-path-length MIN_PATH_LENGTH Minimum path length
Example:
BrainConnect fusion \ --features results/features.csv \ --experiment-results data/experiment_data/result/merged_results.csv \ --output results/fusion_results.csv
Train Model:
BrainConnect model [-h] --fusion-results FUSION_RESULTS --gene-data GENE_DATA --output OUTPUT [--acro-dict ACRO_DICT] [--window-size WINDOW_SIZE] [--epochs EPOCHS] [--batch-size BATCH_SIZE]
options: -h, --help show this help message and exit --fusion-results FUSION_RESULTS, -f FUSION_RESULTS Data fusion results file path --gene-data GENE_DATA, -g GENE_DATA Gene data file path --output OUTPUT, -o OUTPUT Output gene importance file path --output_model OUTPUT_MODEL, -O OUTPUT_MODEL Output model file path (optional) --output_start_to_end_prediction OUTPUT_START_TO_END_PREDICTION, -p OUTPUT_START_TO_END_PREDICTION Output all dataset predictions from start to end (optional) --acro-dict ACRO_DICT Acronym dictionary file path --window-size WINDOW_SIZE Sliding window size --epochs EPOCHS Training epochs --batch-size BATCH_SIZE Batch size
Example:
BrainConnect model \ --fusion-results results/fusion_results.csv \ --gene-data data/gene_data.csv \ --output results/gene_importance.csv
-h, --help: Show help message and exit-v, --version: Show program's version number and exit
Download Allen experimental data
BrainConnect download --experiments <file> --download-dir <dir> --annotation <file> [--limit N]Preprocess experimental data
BrainConnect preprocess --experiments <file> --download-dir <dir> --annotation <file> --output-dir <dir>Process SWC files and analyze neuronal structures
BrainConnect swc --annotation <file> --input <dir> --output <file> [--resolution 25]Extract and integrate neuronal features
BrainConnect feature --swc-results <file> --adjacency <file> --output <file>Perform multimodal data fusion
BrainConnect fusion --features <file> --experiment-results <file> --output <file>Train machine learning models and predict gene importance
BrainConnect model --fusion-results <file> --gene-data <file> --output <file>annotation_25.nrrd: Brain region annotation fileexperiments.csv: Experimental data metadataadjacency_matrix.csv: Brain region connectivity matrixgene_data.csv: Gene expression data- SWC files in organized directory structure
swc_results.csv: Processed SWC file resultsfeatures.csv: Extracted neuronal featuresfusion_results.csv: Fused multimodal datagene_importance.csv: Gene importance rankings
Default configuration can be viewed using:
fromBrainConnectimportConfigConfig.show_info()- Python 3.12+
- pandas
- numpy
- tensorflow
- pyswcloader
- networkx
For issues and questions, please contact: 1984607077@qq.com