spPipline

spatial data (dartfish) processing and analysis

Installation

Requirements

• SimpleElastix
• FIJI
• Cellpose

• 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