digraph snakemake_dag { graph[bgcolor=white, margin=0]; node[shape=box, style=rounded, fontname=sans, fontsize=10, penwidth=2]; edge[penwidth=2, color=grey]; 0 [ shape=none, margin=0, label=<

push_atlas_datasets

↪ input
leaves_only/pushed_atlas_release.log
leaves_only/pushed_cellComposition.log
leaves_only/pushed_meshes.log
leaves_only/pushed_volumetric_datasets.log

output →
leaves_only/pushed_atlas_datasets.log

>] 1 [ shape=none, margin=0, label=<

push_atlas_release

↪ input
leaves_only/annotation_ccfv3_l23split_barrelsplit_validated.nrrd
leaves_only/cell_orientations.nrrd
leaves_only/direction_vectors/direction_vectors_ccfv3.nrrd
leaves_only/hemispheres_annotation.nrrd
leaves_only/mba_hierarchy.json
leaves_only/mba_hierarchy_ld.json
leaves_only/placement_hints
leaves_only/placement_hints/metadata.json
metadata/PH_layers_regions_map.json

output →
leaves_only/pushed_atlas_release.log

>] 2 [ shape=none, margin=0, label=<

export_brain_region

↪ input
leaves_only/annotation_ccfv3_l23split_barrelsplit_validated.nrrd
leaves_only/hierarchy_ccfv3_l23split_barrelsplit.json
leaves_only/regions_layers_map.json

output →
leaves_only/brain_region_mask
leaves_only/brain_region_mesh
leaves_only/mba_hierarchy.json
leaves_only/mba_hierarchy_ld.json
leaves_only/metadata_parcellations.json

>] 3 [ shape=none, margin=0, label=<

split_barrel_ccfv3_l23split

↪ input
leaves_only/annotation_ccfv3_leaves_only.nrrd
leaves_only/barrel_positions_25.feather
leaves_only/hierarchy_ccfv3_leaves_only.json

output →
leaves_only/annotation_ccfv3_l23split_barrelsplit.nrrd
leaves_only/hierarchy_ccfv3_l23split_barrelsplit.json

>] 4 [ shape=none, margin=0, label=<

create_leaves_only_hierarchy_annotation_ccfv3

↪ input
leaves_only/annotation_ccfv3_l23split.nrrd
leaves_only/hierarchy_ccfv3_l23split.json

output →
leaves_only/annotation_ccfv3_leaves_only.nrrd
leaves_only/hierarchy_ccfv3_leaves_only.json

>] 5 [ shape=none, margin=0, label=<

split_isocortex_layer_23_ccfv3

↪ input
leaves_only/annotation_ccfv3.nrrd
leaves_only/direction_vectors/direction_vectors_isocortex_ccfv3.nrrd
leaves_only/hierarchy.json

output →
leaves_only/annotation_ccfv3_l23split.nrrd
leaves_only/hierarchy_ccfv3_l23split.json

>] 6 [ shape=none, margin=0, label=<

fetch_ccf_brain_region_hierarchy

output →
leaves_only/hierarchy.json

>] 7 [ shape=none, margin=0, label=<

fetch_brain_parcellation_ccfv3

output →
leaves_only/annotation_ccfv3.nrrd

>] 8 [ shape=none, margin=0, label=<

direction_vectors_isocortex_ccfv3

↪ input
leaves_only/annotation_ccfv3.nrrd
leaves_only/hierarchy.json

output →
leaves_only/direction_vectors/direction_vectors_isocortex_ccfv3.nrrd

>] 9 [ shape=none, margin=0, label=<

fetch_barrel_positions

output →
leaves_only/barrel_positions_25.feather

>] 10 [ shape=none, margin=0, label=<

validate_annotation_v3

↪ input
leaves_only/annotation_ccfv3_l23split_barrelsplit.nrrd

output →
leaves_only/annotation_ccfv3_l23split_barrelsplit_validated.nrrd

>] 11 [ shape=none, margin=0, label=<

fetch_regions_layers_map

output →
leaves_only/regions_layers_map.json

>] 12 [ shape=none, margin=0, label=<

create_hemispheres_ccfv3

↪ input
leaves_only/annotation_ccfv3_l23split_barrelsplit_validated.nrrd

output →
leaves_only/hemispheres_annotation.nrrd

>] 13 [ shape=none, margin=0, label=<

placement_hints

↪ input
leaves_only/annotation_ccfv3_l23split_barrelsplit_validated.nrrd
leaves_only/direction_vectors/direction_vectors_ccfv3.nrrd
leaves_only/hierarchy_ccfv3_l23split_barrelsplit.json
leaves_only/isocortex_metadata.json

output →
leaves_only/placement_hints
leaves_only/placement_hints/metadata.json

>] 14 [ shape=none, margin=0, label=<

fetch_isocortex_metadata

output →
leaves_only/isocortex_metadata.json

>] 15 [ shape=none, margin=0, label=<

direction_vectors_default_ccfv3

↪ input
leaves_only/annotation_ccfv3.nrrd
leaves_only/hierarchy.json

output →
leaves_only/direction_vectors
leaves_only/direction_vectors/direction_vectors_ccfv3.nrrd

>] 16 [ shape=none, margin=0, label=<

orientation_field

↪ input
leaves_only/direction_vectors/direction_vectors_ccfv3.nrrd

output →
leaves_only/cell_orientations.nrrd

>] 17 [ shape=none, margin=0, label=<

push_meshes

↪ input
leaves_only/brain_region_mesh
leaves_only/mba_hierarchy.json

output →
leaves_only/pushed_meshes.log

>] 18 [ shape=none, margin=0, label=<

push_volumetric_datasets

↪ input
leaves_only/pushed_inhibitory_neuron_densities.log
leaves_only/pushed_masks.log
leaves_only/pushed_metype_datasets.log
leaves_only/pushed_neuron_glia_densities.log

output →
leaves_only/pushed_volumetric_datasets.log

>] 19 [ shape=none, margin=0, label=<

push_masks

↪ input
leaves_only/brain_region_mask
leaves_only/mba_hierarchy.json

output →
leaves_only/pushed_masks.log

>] 20 [ shape=none, margin=0, label=<

push_neuron_glia_densities

↪ input
leaves_only/cell_densities_correctednissl_validated
leaves_only/hierarchy_ccfv3_l23split_barrelsplit.json

output →
leaves_only/pushed_neuron_glia_densities.log

>] 21 [ shape=none, margin=0, label=<

validate_neuron_glia_cell_densities

↪ input
leaves_only/annotation_ccfv3_l23split_barrelsplit_validated.nrrd
leaves_only/cell_densities_correctednissl

output →
leaves_only/cell_densities_correctednissl_validated
leaves_only/cell_densities_correctednissl_validated/neuron_density.nrrd

>] 22 [ shape=none, margin=0, label=<

glia_cell_densities_correctednissl

↪ input
leaves_only/annotation_ccfv3_l23split_barrelsplit_validated.nrrd
leaves_only/astrocyte.nrrd
leaves_only/glia.nrrd
leaves_only/glia_proportions.json
leaves_only/hierarchy_ccfv3_l23split_barrelsplit.json
leaves_only/microglia.nrrd
leaves_only/oligodendrocyte.nrrd
leaves_only/overall_cell_density_correctednissl_validated.nrrd
leaves_only/rules_config_dir/regions_groups.json

output →
leaves_only/cell_densities_correctednissl
leaves_only/cell_densities_correctednissl/astrocyte_density.nrrd
leaves_only/cell_densities_correctednissl/glia_density.nrrd
leaves_only/cell_densities_correctednissl/microglia_density.nrrd
leaves_only/cell_densities_correctednissl/neuron_density.nrrd
leaves_only/cell_densities_correctednissl/oligodendrocyte_density.nrrd

>] 23 [ shape=none, margin=0, label=<

validate_cell_density

↪ input
leaves_only/annotation_ccfv3_l23split_barrelsplit_validated.nrrd
leaves_only/overall_cell_density_correctednissl.nrrd

output →
leaves_only/overall_cell_density_correctednissl_validated.nrrd

>] 24 [ shape=none, margin=0, label=<

cell_density_correctednissl

↪ input
leaves_only/annotation_ccfv3_l23split_barrelsplit_validated.nrrd
leaves_only/hierarchy_ccfv3_l23split_barrelsplit.json
leaves_only/nissl_corrected_volume.nrrd
leaves_only/rules_config_dir/regions_groups.json

output →
leaves_only/overall_cell_density_correctednissl.nrrd

>] 25 [ shape=none, margin=0, label=<

fetch_corrected_nissl_stained_volume

output →
leaves_only/nissl_corrected_volume.nrrd

>] 26 [ shape=none, margin=0, label=<

fetch_regions_config

output →
leaves_only/rules_config_dir/regions_groups.json

>] 27 [ shape=none, margin=0, label=<

combine_markers

↪ input
leaves_only/annotation_ccfv3_l23split_barrelsplit_validated.nrrd
leaves_only/gene_aldh1l1.nrrd
leaves_only/gene_cnp.nrrd
leaves_only/gene_gfap.nrrd
leaves_only/gene_mbp.nrrd
leaves_only/gene_s100b.nrrd
leaves_only/gene_tmem119.nrrd
leaves_only/hierarchy_ccfv3_l23split_barrelsplit.json

output →
leaves_only/astrocyte.nrrd
leaves_only/glia.nrrd
leaves_only/glia_proportions.json
leaves_only/microglia.nrrd
leaves_only/oligodendrocyte.nrrd

>] 28 [ shape=none, margin=0, label=<

fetch_gene_aldh1l1

output →
leaves_only/gene_aldh1l1.nrrd

>] 29 [ shape=none, margin=0, label=<

fetch_gene_cnp

output →
leaves_only/gene_cnp.nrrd

>] 30 [ shape=none, margin=0, label=<

fetch_gene_mbp

output →
leaves_only/gene_mbp.nrrd

>] 31 [ shape=none, margin=0, label=<

fetch_gene_gfap

output →
leaves_only/gene_gfap.nrrd

>] 32 [ shape=none, margin=0, label=<

fetch_gene_s100b

output →
leaves_only/gene_s100b.nrrd

>] 33 [ shape=none, margin=0, label=<

fetch_gene_tmem119

output →
leaves_only/gene_tmem119.nrrd

>] 34 [ shape=none, margin=0, label=<

push_inhibitory_neuron_densities

↪ input
leaves_only/hierarchy_ccfv3_l23split_barrelsplit.json
leaves_only/inhibitory_neuron_densities_linprog_correctednissl_validated

output →
leaves_only/pushed_inhibitory_neuron_densities.log

>] 35 [ shape=none, margin=0, label=<

validate_inhibitory_densities

↪ input
leaves_only/annotation_ccfv3_l23split_barrelsplit_validated.nrrd
leaves_only/cell_densities_correctednissl_validated
leaves_only/hierarchy_ccfv3_l23split_barrelsplit.json
leaves_only/inhibitory_neuron_densities_linprog_correctednissl
leaves_only/overall_cell_density_correctednissl_validated.nrrd

output →
leaves_only/inhibitory_neuron_densities_linprog_correctednissl_validated

>] 36 [ shape=none, margin=0, label=<

inhibitory_neuron_densities_linprog_correctednissl

↪ input
leaves_only/annotation_ccfv3_l23split_barrelsplit_validated.nrrd
leaves_only/cell_densities_correctednissl_validated/neuron_density.nrrd
leaves_only/fitted_densities_correctednissl.csv
leaves_only/hierarchy_ccfv3_l23split_barrelsplit.json

output →
leaves_only/inhibitory_neuron_densities_linprog_correctednissl

>] 37 [ shape=none, margin=0, label=<

fit_average_densities_correctednissl

↪ input
leaves_only/annotation_ccfv3_l23split_barrelsplit_validated.nrrd
leaves_only/average_cell_densities_correctednissl.csv
leaves_only/cell_densities_correctednissl_validated/neuron_density.nrrd
leaves_only/fetched_genes_correctednissl.log
leaves_only/hierarchy_ccfv3_l23split_barrelsplit.json
leaves_only/rules_config_dir/fit_average_densities_correctednissl_config.yaml
leaves_only/rules_config_dir/homogenous_regions.csv
leaves_only/rules_config_dir/realigned_slices.json
leaves_only/rules_config_dir/regions_groups.json
leaves_only/rules_config_dir/std_cells.json

output →
leaves_only/fitted_densities_correctednissl.csv
leaves_only/fitting_maps_correctednissl.json

>] 38 [ shape=none, margin=0, label=<

fetch_genes_correctednissl

↪ input
leaves_only/gene_gad67_correctednissl.nrrd
leaves_only/gene_pv_correctednissl.nrrd
leaves_only/gene_sst_correctednissl.nrrd
leaves_only/gene_vip_correctednissl.nrrd

output →
leaves_only/fetched_genes_correctednissl.log

>] 39 [ shape=none, margin=0, label=<

fetch_gene_pv_correctednissl

output →
leaves_only/gene_pv_correctednissl.nrrd

>] 40 [ shape=none, margin=0, label=<

fetch_gene_sst_correctednissl

output →
leaves_only/gene_sst_correctednissl.nrrd

>] 41 [ shape=none, margin=0, label=<

fetch_gene_vip_correctednissl

output →
leaves_only/gene_vip_correctednissl.nrrd

>] 42 [ shape=none, margin=0, label=<

fetch_gene_gad67_correctednissl

output →
leaves_only/gene_gad67_correctednissl.nrrd

>] 43 [ shape=none, margin=0, label=<

fetch_realigned_slices

output →
leaves_only/rules_config_dir/realigned_slices.json

>] 44 [ shape=none, margin=0, label=<

fetch_std_cells

output →
leaves_only/rules_config_dir/std_cells.json

>] 45 [ shape=none, margin=0, label=<

average_densities_correctednissl

↪ input
leaves_only/annotation_ccfv3_l23split_barrelsplit_validated.nrrd
leaves_only/cell_densities_correctednissl_validated/neuron_density.nrrd
leaves_only/hierarchy_ccfv3_l23split_barrelsplit.json
leaves_only/overall_cell_density_correctednissl_validated.nrrd
leaves_only/rules_config_dir/measurements.csv

output →
leaves_only/average_cell_densities_correctednissl.csv

>] 46 [ shape=none, margin=0, label=<

fetch_measurements

output →
leaves_only/rules_config_dir/measurements.csv

>] 47 [ shape=none, margin=0, label=<

fetch_homogenous_regions

output →
leaves_only/rules_config_dir/homogenous_regions.csv

>] 48 [ shape=none, margin=0, label=<

push_metype_pipeline_datasets

↪ input
leaves_only/excitatory_split_validated
leaves_only/hierarchy_ccfv3_l23split_barrelsplit.json
leaves_only/mtypes_densities_probability_map_validated

output →
leaves_only/pushed_metype_datasets.log

>] 49 [ shape=none, margin=0, label=<

validate_all_ME_densities

↪ input
leaves_only/annotation_ccfv3_l23split_barrelsplit_validated.nrrd
leaves_only/excitatory_split
leaves_only/mtypes_densities_probability_map

output →
leaves_only/excitatory_split_validated
leaves_only/mtypes_densities_probability_map_validated

>] 50 [ shape=none, margin=0, label=<

create_mtypes_densities_from_probability_map

↪ input
leaves_only/annotation_ccfv3_l23split_barrelsplit_validated.nrrd
leaves_only/hierarchy_ccfv3_l23split_barrelsplit.json
leaves_only/inhibitory_neuron_densities_linprog_correctednissl_validated
leaves_only/lamp5_density.nrrd
leaves_only/rules_config_dir/mtypes/probability_map_L1.csv
leaves_only/rules_config_dir/mtypes/probability_map_L23.csv
leaves_only/rules_config_dir/mtypes/probability_map_L4.csv
leaves_only/rules_config_dir/mtypes/probability_map_L5.csv
leaves_only/rules_config_dir/mtypes/probability_map_L6.csv
leaves_only/rules_config_dir/mtypes/probability_map_TH_INH.csv

output →
leaves_only/mtypes_densities_probability_map

>] 51 [ shape=none, margin=0, label=<

fetch_probability_map_L1

output →
leaves_only/rules_config_dir/mtypes/probability_map_L1.csv

>] 52 [ shape=none, margin=0, label=<

fetch_probability_map_L23

output →
leaves_only/rules_config_dir/mtypes/probability_map_L23.csv

>] 53 [ shape=none, margin=0, label=<

fetch_probability_map_L4

output →
leaves_only/rules_config_dir/mtypes/probability_map_L4.csv

>] 54 [ shape=none, margin=0, label=<

fetch_probability_map_L5

output →
leaves_only/rules_config_dir/mtypes/probability_map_L5.csv

>] 55 [ shape=none, margin=0, label=<

fetch_probability_map_L6

output →
leaves_only/rules_config_dir/mtypes/probability_map_L6.csv

>] 56 [ shape=none, margin=0, label=<

fetch_probability_map_TH_INH

output →
leaves_only/rules_config_dir/mtypes/probability_map_TH_INH.csv

>] 57 [ shape=none, margin=0, label=<

compute_lamp5_density

↪ input
leaves_only/inhibitory_neuron_densities_linprog_correctednissl_validated

output →
leaves_only/lamp5_density.nrrd

>] 58 [ shape=none, margin=0, label=<

excitatory_split

↪ input
leaves_only/annotation_ccfv3_l23split_barrelsplit_validated.nrrd
leaves_only/cell_densities_correctednissl_validated/neuron_density.nrrd
leaves_only/hierarchy_ccfv3_l23split_barrelsplit.json
leaves_only/inhibitory_neuron_densities_linprog_correctednissl_validated
leaves_only/isocortex_metadata.json
leaves_only/mapping_cortex_all_to_exc_mtypes.csv

output →
leaves_only/excitatory_split

>] 59 [ shape=none, margin=0, label=<

fetch_mapping_cortex_all_to_exc_mtypes

output →
leaves_only/mapping_cortex_all_to_exc_mtypes.csv

>] 60 [ shape=none, margin=0, label=<

push_cellComposition

↪ input
leaves_only/cellCompositionSummary_payload_staging.json
leaves_only/cellCompositionVolume_payload_staging.json
leaves_only/hierarchy_ccfv3_l23split_barrelsplit.json

output →
leaves_only/pushed_cellComposition.log

>] 61 [ shape=none, margin=0, label=<

create_cellCompositionVolume_payload

↪ input
leaves_only/pushed_metype_datasets.log

output →
leaves_only/cellCompositionVolume_payload_staging.json

>] 62 [ shape=none, margin=0, label=<

create_cellCompositionSummary_payload

↪ input
leaves_only/annotation_ccfv3_l23split_barrelsplit_validated.nrrd
leaves_only/cellCompositionVolume_payload_staging.json
leaves_only/hierarchy_ccfv3_l23split_barrelsplit.json

output →
leaves_only/cellCompositionSummary_payload_staging.json
leaves_only/density_distribution_staging.json

>] 60 -> 0 17 -> 0 18 -> 0 1 -> 0 10 -> 1 13 -> 1 2 -> 1 15 -> 1 16 -> 1 12 -> 1 10 -> 2 3 -> 2 11 -> 2 4 -> 3 9 -> 3 5 -> 4 6 -> 5 8 -> 5 7 -> 5 6 -> 8 7 -> 8 3 -> 10 10 -> 12 15 -> 13 10 -> 13 3 -> 13 14 -> 13 6 -> 15 7 -> 15 15 -> 16 2 -> 17 19 -> 18 20 -> 18 48 -> 18 34 -> 18 2 -> 19 3 -> 20 21 -> 20 10 -> 21 22 -> 21 27 -> 22 10 -> 22 3 -> 22 23 -> 22 26 -> 22 10 -> 23 24 -> 23 10 -> 24 3 -> 24 25 -> 24 26 -> 24 10 -> 27 33 -> 27 3 -> 27 30 -> 27 29 -> 27 28 -> 27 32 -> 27 31 -> 27 35 -> 34 3 -> 34 10 -> 35 3 -> 35 23 -> 35 36 -> 35 21 -> 35 10 -> 36 3 -> 36 37 -> 36 21 -> 36 10 -> 37 44 -> 37 38 -> 37 3 -> 37 47 -> 37 43 -> 37 45 -> 37 21 -> 37 26 -> 37 40 -> 38 42 -> 38 41 -> 38 39 -> 38 10 -> 45 46 -> 45 3 -> 45 23 -> 45 21 -> 45 49 -> 48 3 -> 48 10 -> 49 50 -> 49 58 -> 49 10 -> 50 56 -> 50 51 -> 50 35 -> 50 55 -> 50 3 -> 50 53 -> 50 52 -> 50 54 -> 50 57 -> 50 35 -> 57 10 -> 58 14 -> 58 35 -> 58 3 -> 58 59 -> 58 21 -> 58 61 -> 60 3 -> 60 62 -> 60 48 -> 61 10 -> 62 3 -> 62 61 -> 62 }