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spPipline

spatial data (dartfish) processing and analysis

Installation

Requirements

  • for current version, you can clone the github repository
git clone https://github.com/huqiwen0313/spPipline.git
cd spPipline

Usage

  1. Copy "_codebook" to the output path
  2. Run processing pipelines
cd spPipline
python -m spPipline [arguments]
Arguments Description default
-r or --raw input path of Raw files. "../0_Raw"
-o or --output output path contains processed files. "./"
-s or --sigma sigma value for gaussian filter. 0.7
-rd or --rnd_list list of decoding cycle rounds. ["0_anchor", "1_dc0", "2_dc1", "3_dc2", "4_dc3", "5_dc4", "6_dc5", "7_DRAQ5"]
-nf or --nfovs number of fov (filed of view) 80
-cr or --channel_DIC_reference DIC channel for reference cycle 'ch03'
-cd or --channel_DIC DIC channel for (non-reference) decoding cycles 'ch03'
-co or ----cycle_other other data-containing folders which need to be aligned but are not names 'CycleXX' ['0_anchor', '7_DRAQ5']
-cdo or --channel_DIC_other DIC channel for other data-containing folders {'0_anchor': 'ch01', '7_DRAQ5': 'ch01'}
-gx or --grid_size_x grid size (x-axis) for each tile 8
-gy or --grid_size_y grid size (y-axis) for each tile 10
-to or --tile_overlap overlap for each tile 15
-ij or --ij_path The path to imagej’s executables "/home/qiwenhu/software/Fiji.app/ImageJ-linux64" (need to set with your own path)
-sr or --stitchRef The round to be used as the reference for stitching "dc3"

output file structure (processed data)

Example:

SAMPLE (BUKMAP_20200303F_DFv1_ROI1)
    ├── _codebook
    ├── 1_Projected
    ├── 2_Registered
    │   ├── stitched
    │   └── FOVs
    ├── 3_Decoded
    │   ├── output_Starfish
    │   └── data_Starfish
    └── 4_CellAssignment