brainlit
Brainlit
Motivation
Installation
Environment
Install from pypi
Install from source
Common Installation Issues
How to use Brainlit
Data setup
Create a session
Features
Registration
Core
Push and Pull Data
Visualize
Manually Segment
Automatically and Semi-automatically Segment
Tests
Contributing
Credits
Tutorial
Utils
Uploading Brain Images from data in the Octree format.
Downloading Brain data tutorial
Download benchmarking data from S3 with Neuroglancer
Download raw benchmarking data
Upload benchmarking data to S3 with Neuroglancer
Pipelines
Semi-automatic Annotation Pipeline
Segmentation
Algorithms
Adaptive Thresholding
Connecting Fragments
Trace Analysis
Soma Detection
Preprocessing
Connected Component Manipulation
Gabor Filters
Vizualization
Loading neurons from s3
Visualization of Neighborhoods Tutorial
Reference
Algorithms
Fragment Generation
Connect Fragments
Trace Analysis
Soma Detection
Feature Extraction
NeighborhoodFeatures
Preprocessing
Image Processing
Image Filters
Segmentation Processing
Registration
File IO
Image Data
Transformers
Visualization
Utility
Data Helper Methods
S3 Helper Methods
Visualization
Trace Visualization
Napari Plugin
ViterBrain Napari Plugin Installation
How to Use the ViterBrain Napari Plugin
License
Publication Related Code
Fitting Splines to Axonal Arbors Quantifies Relationship between Branch Order and Geometry
Publication
How to reproduce this experiment
Hidden Markov Modeling for Maximum Likelihood Neuron Reconstruction
Manuscript
How to use ViterBrain
Useful Links
Brainlit @ GitHub
Issue Tracker
brainlit
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Index
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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H
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I
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
A
args (brainlit.utils.NeuronTrace attribute)
B
Bresenham3D() (in module brainlit.viz)
C
center() (in module brainlit.preprocessing)
chunk_size (brainlit.utils.NeuroglancerSession attribute)
compute_all_costs_dist() (brainlit.algorithms.connect_fragments.ViterBrain method)
compute_all_costs_int() (brainlit.algorithms.connect_fragments.ViterBrain method)
compute_bfs() (brainlit.algorithms.generate_fragments.state_generation method)
compute_edge_weights() (brainlit.algorithms.generate_fragments.state_generation method)
compute_frags() (brainlit.algorithms.generate_fragments.state_generation method)
(in module brainlit.preprocessing)
compute_image_tiered() (brainlit.algorithms.generate_fragments.state_generation method)
compute_soma_lbls() (brainlit.algorithms.generate_fragments.state_generation method)
compute_states() (brainlit.algorithms.generate_fragments.state_generation method)
confidence_connected_threshold() (in module brainlit.algorithms.generate_fragments)
connected_threshold() (in module brainlit.algorithms.generate_fragments)
continue_registration() (brainlit.registration.Transform method)
contrast_normalize() (in module brainlit.preprocessing)
conversion_time (brainlit.feature_extraction.NeighborhoodFeatures attribute)
create_tubes() (brainlit.utils.NeuroglancerSession method)
curvature() (in module brainlit.algorithms.trace_analysis)
cv (brainlit.utils.NeuroglancerSession attribute)
cv_annotations (brainlit.utils.NeuroglancerSession attribute)
cv_segments (brainlit.utils.NeuroglancerSession attribute)
D
df (brainlit.utils.NeuronTrace attribute)
download_time (brainlit.feature_extraction.NeighborhoodFeatures attribute)
F
fast_marching_seg() (in module brainlit.algorithms.generate_fragments)
find_somas() (in module brainlit.algorithms.detect_somas)
fit_spline_tree_invariant() (brainlit.algorithms.trace_analysis.GeometricGraph method)
frag_frag_dist() (brainlit.algorithms.connect_fragments.ViterBrain method)
frag_soma_dist() (brainlit.algorithms.connect_fragments.ViterBrain method)
G
gabor_filter() (in module brainlit.preprocessing)
generate_df_subset() (brainlit.utils.NeuronTrace method)
GeometricGraph (class in brainlit.algorithms.trace_analysis)
get_bfs_subgraph() (brainlit.utils.NeuronTrace method)
get_df() (brainlit.utils.NeuronTrace method)
get_df_arguments() (brainlit.utils.NeuronTrace method)
get_df_voxel() (brainlit.utils.NeuronTrace method)
get_graph() (brainlit.utils.NeuronTrace method)
get_img_T1() (in module brainlit.algorithms.generate_fragments)
get_lddmm_dict() (brainlit.registration.Transform method)
get_paths() (brainlit.utils.NeuronTrace method)
get_seed() (in module brainlit.algorithms.generate_fragments)
get_segments() (brainlit.utils.NeuroglancerSession method)
get_skel() (brainlit.utils.NeuronTrace method)
get_sub_neuron() (brainlit.utils.NeuronTrace method)
get_sub_neuron_paths() (brainlit.utils.NeuronTrace method)
getLargestCC() (in module brainlit.preprocessing)
gmm_seg() (in module brainlit.algorithms.generate_fragments)
H
heatslices() (in module brainlit.registration)
I
imagize_vector() (in module brainlit.preprocessing)
input_type (brainlit.utils.NeuronTrace attribute)
L
label_points() (in module brainlit.preprocessing)
level_set_seg() (in module brainlit.algorithms.generate_fragments)
load() (brainlit.registration.Transform method)
(in module brainlit.registration)
M
mip (brainlit.utils.NeuroglancerSession attribute)
(brainlit.utils.NeuronTrace attribute)
N
neighborhood_connected_threshold() (in module brainlit.algorithms.generate_fragments)
NeighborhoodFeatures (class in brainlit.feature_extraction)
NeuroglancerSession (class in brainlit.utils)
NeuronTrace (class in brainlit.utils)
O
offset (brainlit.feature_extraction.NeighborhoodFeatures attribute)
otsu() (in module brainlit.algorithms.generate_fragments)
P
path (brainlit.utils.NeuronTrace attribute)
point_threshold() (in module brainlit.viz)
predict() (brainlit.algorithms.generate_fragments.state_generation method)
pull_bounds_img() (brainlit.utils.NeuroglancerSession method)
pull_bounds_seg() (brainlit.utils.NeuroglancerSession method)
pull_chunk() (brainlit.utils.NeuroglancerSession method)
pull_vertex_list() (brainlit.utils.NeuroglancerSession method)
pull_voxel() (brainlit.utils.NeuroglancerSession method)
push() (brainlit.utils.NeuroglancerSession method)
R
register() (brainlit.registration.Transform method)
remove_somas() (in module brainlit.preprocessing)
removeSmallCCs() (in module brainlit.preprocessing)
rename_states_consecutively() (in module brainlit.preprocessing)
S
save() (brainlit.registration.Transform method)
(in module brainlit.registration)
scales (brainlit.utils.NeuroglancerSession attribute)
seg_id (brainlit.utils.NeuronTrace attribute)
segment_url (brainlit.feature_extraction.NeighborhoodFeatures attribute)
set_url_segments() (brainlit.utils.NeuroglancerSession method)
shortest_path() (brainlit.algorithms.connect_fragments.ViterBrain method)
size (brainlit.feature_extraction.NeighborhoodFeatures attribute)
skeleton_threshold_intersect() (in module brainlit.viz)
skeletonize() (in module brainlit.viz)
snap_points() (in module brainlit.viz)
speed() (in module brainlit.algorithms.trace_analysis)
ssd() (brainlit.utils.NeuronTrace static method)
state_generation (class in brainlit.algorithms.generate_fragments)
T
thres_from_gmm() (in module brainlit.algorithms.generate_fragments)
torsion() (in module brainlit.algorithms.trace_analysis)
Transform (class in brainlit.registration)
transform_image() (brainlit.registration.Transform method)
transform_points() (brainlit.registration.Transform method)
U
undo_pad() (in module brainlit.preprocessing)
url (brainlit.feature_extraction.NeighborhoodFeatures attribute)
(brainlit.utils.NeuroglancerSession attribute)
url_segments (brainlit.utils.NeuroglancerSession attribute)
V
vectorize_img() (in module brainlit.preprocessing)
ViterBrain (class in brainlit.algorithms.connect_fragments)
W
whiten() (in module brainlit.preprocessing)
window_pad() (in module brainlit.preprocessing)
write_time (brainlit.feature_extraction.NeighborhoodFeatures attribute)