BrainConnect 1.0.1

Step-by-Step Workflow

1. 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

2. 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

3. 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

4. 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

5. 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

6. 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

Global Options

• -h, --help: Show help message and exit

• -v, --version: Show program’s version number and exit

Available Commands

BrainConnect download --experiments <file> --download-dir <dir> --annotation <file> [--limit N]

BrainConnect preprocess --experiments <file> --download-dir <dir> --annotation <file> --output-dir <dir>

BrainConnect swc --annotation <file> --input <dir> --output <file> [--resolution 25]

BrainConnect feature --swc-results <file> --adjacency <file> --output <file>

BrainConnect fusion --features <file> --experiment-results <file> --output <file>

BrainConnect model --fusion-results <file> --gene-data <file> --output <file>

Input Files

• annotation_25.nrrd: Brain region annotation file

• experiments.csv: Experimental data metadata

• adjacency_matrix.csv: Brain region connectivity matrix

• gene_data.csv: Gene expression data

• SWC files in organized directory structure

Output Files

• swc_results.csv: Processed SWC file results

• features.csv: Extracted neuronal features

• fusion_results.csv: Fused multimodal data

• gene_importance.csv: Gene importance rankings