Single Image Analysis Pipeline

Loading in all relevant packages

from cellcounter.pipelines.pipeline_funcs import (
    cell_mapping_pipeline,
    cellc1_pipeline,
    cellc2_pipeline,
    cellc3_pipeline,
    cellc4_pipeline,
    cellc5_pipeline,
    cellc6_pipeline,
    cellc7_pipeline,
    cellc8_pipeline,
    cellc9_pipeline,
    cellc10_pipeline,
    cellc11_pipeline,
    cellc_coords_only_pipeline,
    cells2csv_pipeline,
    coords2points_raw_pipeline,
    coords2points_trfm_pipeline,
    group_cells_pipeline,
    img_fine_pipeline,
    img_overlap_pipeline,
    img_rough_pipeline,
    img_trim_pipeline,
    make_mask_pipeline,
    ref_prepare_pipeline,
    registration_pipeline,
    tiff2zarr_pipeline,
    transform_coords_pipeline,
)
from cellcounter.utils.proj_org_utils import (
    get_proj_fp_model,
    update_configs,
)

Set the input filename/folder and project folder to use

in_fp = "/path/to/input_file.tiff"
proj_dir = "/path/to/proj_dir"

Load project object

pfm = get_proj_fp_model(proj_dir)

Update configs

Also see Configs for more parameters to modify and their descriptions.

update_configs(
    pfm,
    # REFERENCE
    # RAW
    # REGISTRATION
    ref_orient_ls=(-2, 3, 1),
    ref_z_trim=(None, None, None),
    ref_y_trim=(None, None, None),
    ref_x_trim=(None, None, None),
    z_rough=3,
    y_rough=6,
    x_rough=6,
    z_fine=1,
    y_fine=0.6,
    x_fine=0.6,
    z_trim=(None, None, None),
    y_trim=(None, None, None),
    x_trim=(None, None, None),
    # MASK
    # OVERLAP
    # CELL COUNTING
    tophat_sigma=10,
    dog_sigma1=1,
    dog_sigma2=4,
    gauss_sigma=101,
    thresh_p=60,
    min_threshd=100,
    max_threshd=9000,
    maxima_sigma=10,
    min_wshed=1,
    max_wshed=700,
)

Run Pipeline

For more information, see Pipeline

Single line version

all_pipeline(pfm, in_fp, overwrite=overwrite)

Manually run each function version

# Making zarr from tiff file(s)
tiff2zarr_pipeline(pfm, in_fp, overwrite=overwrite)
# Preparing reference images
ref_prepare_pipeline(pfm, overwrite=overwrite)
# Preparing image itself
img_rough_pipeline(pfm, overwrite=overwrite)
img_fine_pipeline(pfm, overwrite=overwrite)
img_trim_pipeline(pfm, overwrite=overwrite)
# Running Elastix registration
registration_pipeline(pfm, overwrite=overwrite)
# Running mask pipeline
make_mask_pipeline(pfm, overwrite=overwrite)
# Making overlap chunks in preparation for cell counting
img_overlap_pipeline(pfm, overwrite=overwrite)
# Counting cells
cellc1_pipeline(pfm, overwrite=overwrite)
cellc2_pipeline(pfm, overwrite=overwrite)
cellc3_pipeline(pfm, overwrite=overwrite)
cellc4_pipeline(pfm, overwrite=overwrite)
cellc5_pipeline(pfm, overwrite=overwrite)
cellc6_pipeline(pfm, overwrite=overwrite)
cellc7_pipeline(pfm, overwrite=overwrite)
cellc8_pipeline(pfm, overwrite=overwrite)
cellc9_pipeline(pfm, overwrite=overwrite)
cellc10_pipeline(pfm, overwrite=overwrite)
cellc11_pipeline(pfm, overwrite=overwrite)
cellc_coords_only_pipeline(pfm, overwrite=overwrite)
# Converting maxima from raw space to refernce atlas space
transform_coords_pipeline(pfm, overwrite=overwrite)
# Getting Region ID mappings for each cell
cell_mapping_pipeline(pfm, overwrite=overwrite)
# Grouping cells
group_cells_pipeline(pfm, overwrite=overwrite)
# Exporting cells_agg parquet as csv
cells2csv_pipeline(pfm, overwrite=overwrite)

Optional: Run visual checks

# Running visual checks
coords2points_raw_pipeline(pfm)
coords2points_trfm_pipeline(pfm)