cajal
stable
Overview and Walkthrough
What is CAJAL?
Computing Intracellular Distance Matrices
Computing GW Distances
Inferring Associations with Cell Morphology
Computing Average Cell Shapes
TUTORIALS
Tutorial 1: Predicting the Molecular Type of Neurons
Tutorial 2: Genetic Determinants of Neuronal Morphology
Tutorial 3: Computing Morphological Distances in Very Large Datasets
Tutorial 4: Integration and Analysis of Multimodal Data
API
Processing SWC Files
Sampling from SWC Files
Processing Obj Meshes
Sampling from Segmented Images
Running Gromov-Wasserstein
Second Lower Bound and Quantized Gromov-Wasserstein
Combined SLB and Quantized GW Nearest Neighbors Algorithm
Laplacian Score
Average Cell Shapes
Clustering
Ternary Plots
Weighted Nearest Neighbors
cajal
Index
Edit on GitHub
Index
A
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B
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C
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D
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F
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G
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I
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K
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L
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M
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N
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P
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Q
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R
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S
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T
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W
A
avg_shape() (in module cajal.utilities)
avg_shape_spt() (in module cajal.utilities)
B
batch_filter_and_preprocess() (in module cajal.swc)
C
cajal.combined_slb_qgw
module
cajal.qgw
module
cajal.run_gw.DistanceMatrix (class in src.cajal.run_gw)
cajal.run_gw.Distribution (class in src.cajal.run_gw)
cajal.sample_mesh.FaceArray (class in src.cajal.sample_mesh)
cajal.sample_mesh.VertexArray (class in src.cajal.sample_mesh)
cajal.sample_seg
module
cajal.swc.SWCForest (built-in class)
cell_boundaries() (in module cajal.sample_seg)
cell_iterator() (in module cajal.swc)
cell_iterator_csv() (in module cajal.run_gw)
cell_pair_iterator_csv() (in module cajal.run_gw)
combined_slb_quantized_gw() (in module cajal.combined_slb_qgw)
combined_slb_quantized_gw_memory() (in module cajal.combined_slb_qgw)
compute_gw_distance_matrix() (in module cajal.run_gw)
compute_icdm_all() (in module cajal.sample_mesh)
(in module cajal.sample_seg)
compute_icdm_all_euclidean() (in module cajal.sample_swc)
compute_icdm_all_geodesic() (in module cajal.sample_swc)
D
default_name_validate() (in module cajal.swc)
discrete_depth() (in module cajal.swc)
F
forest_from_linear() (in module cajal.swc)
G
geodesic_distance() (in module cajal.sample_swc)
get_filenames() (in module cajal.swc)
get_sample_pts_euclidean() (in module cajal.sample_swc)
get_sample_pts_geodesic() (in module cajal.sample_swc)
gw_pairwise_parallel() (in module cajal.run_gw)
I
icdm_csv_validate() (in module cajal.run_gw)
icdm_euclidean() (in module cajal.sample_swc)
icdm_geodesic() (in module cajal.sample_swc)
K
keep_only_eu() (in module cajal.swc)
L
laplacian_scores() (in module cajal.laplacian_score)
leiden_clustering() (in module cajal.utilities)
linearize() (in module cajal.swc)
louvain_clustering() (in module cajal.utilities)
M
Modality (class in cajal.wnn)
module
cajal.combined_slb_qgw
cajal.qgw
cajal.sample_seg
src.cajal.run_gw
src.cajal.sample_mesh
N
NeuronNode (class in cajal.swc)
NeuronTree (class in cajal.swc)
node_type_counts_forest() (in module cajal.swc)
node_type_counts_tree() (in module cajal.swc)
num_nodes() (in module cajal.swc)
P
preprocessor_eu() (in module cajal.swc)
preprocessor_geo() (in module cajal.swc)
Q
quantized_gw_parallel() (in module cajal.qgw)
quantized_icdm (class in cajal.qgw)
R
read_obj() (in module cajal.sample_mesh)
read_preprocess_save() (in module cajal.swc)
read_swc() (in module cajal.swc)
S
slb_parallel() (in module cajal.qgw)
slb_parallel_memory() (in module cajal.qgw)
src.cajal.run_gw
module
src.cajal.sample_mesh
module
T
ternary_distance_clusters() (in module cajal.ternary)
total_length() (in module cajal.swc)
W
weighted_depth() (in module cajal.swc)
WeightedTree_of() (in module cajal.weighted_tree)
WeightedTreeChild (class in cajal.weighted_tree)
WeightedTreeRoot (class in cajal.weighted_tree)
wnn() (in module cajal.wnn)
write_swc() (in module cajal.swc)