seung-lab/kimimaro issues and pull requests

#91 - Increasing resolution of the vertex positions to sub-voxel level

Issue - State: open - Opened by RomStriker 4 days ago - 2 comments
Labels: feature

#90 - perf: speed up join close components

Pull Request - State: closed - Opened by peterlionelnewman 3 months ago - 1 comment
Labels: performance

#89 - Kimimaro for skeletonizing collagen fibers - time persistence of skeletons

Issue - State: open - Opened by peterlionelnewman 3 months ago - 2 comments

#88 - Compatibility issue with Igneous' Skeletonization

Issue - State: closed - Opened by SanjeevRJ 3 months ago - 2 comments

#87 - call kimimaro.skeletontricks.roll_invalidation_ball_inside_component using positional-only arguments

Pull Request - State: closed - Opened by jasonkena 4 months ago - 1 comment
Labels: bug

#86 - feat: respect connected components for invalidation + full voxel graph support

Pull Request - State: closed - Opened by william-silversmith 4 months ago
Labels: feature, performance, redesign

#85 - feat: add oversegment function

Pull Request - State: closed - Opened by william-silversmith 6 months ago
Labels: feature

#84 - feat: compute cross sectional area for vertices

Pull Request - State: closed - Opened by william-silversmith 8 months ago
Labels: feature

#83 - parallel is negative, but only use one core

Issue - State: closed - Opened by xiuliren 12 months ago - 5 comments

#82 - increasing number of components

Issue - State: open - Opened by Rajalakshmi-Palaniappan about 1 year ago - 1 comment

#81 - Using kimimaro for voxels skeletonization

Issue - State: open - Opened by ZiYuanZiWan over 1 year ago - 12 comments
Labels: question

#80 - How to choose default TEASER algorithm parameters for processing

Issue - State: open - Opened by liuyx599 over 1 year ago - 1 comment

#79 - Using Kimimaro for vessel skeletonization

Issue - State: open - Opened by RosieFerr over 1 year ago - 1 comment
Labels: question

#78 - Progress bar stopping with parallel

Issue - State: open - Opened by AlexandreDiPiazza over 1 year ago - 7 comments
Labels: bug

#77 - Verbose flag

Issue - State: closed - Opened by 0xJustin over 1 year ago - 3 comments

#76 - Usage on 3D Meshes/Clouds

Issue - State: closed - Opened by eyildiz-ugoe about 2 years ago - 2 comments
Labels: question

#75 - Change in Skeletonisation result with Change in Volume Cropping

Issue - State: closed - Opened by ChristianNikolov about 2 years ago - 11 comments

#74 - Skeleton as Binary 3D Numpy Array

Issue - State: closed - Opened by ChristianNikolov about 2 years ago - 11 comments
Labels: question

#73 - Can't install kimimaro (Windows 64-bit, Python 3.10)

Issue - State: closed - Opened by ChristianNikolov about 2 years ago - 7 comments
Labels: installation

#72 - Make Fixing Avocados Faster

Issue - State: closed - Opened by william-silversmith over 2 years ago
Labels: performance

#71 - How to output the binary 3D skeleton?

Issue - State: closed - Opened by HHHit over 2 years ago - 2 comments
Labels: question

#70 - feat: adds connect_points function

Pull Request - State: closed - Opened by william-silversmith almost 3 years ago
Labels: feature

#69 - Unbranched centerline between suggested points

Issue - State: closed - Opened by urakubo almost 3 years ago - 6 comments
Labels: feature

#68 - Kimimaro History

Issue - State: closed - Opened by william-silversmith about 3 years ago
Labels: documentation

#67 - perf: use the "railroad" technique

Pull Request - State: closed - Opened by william-silversmith about 3 years ago - 4 comments
Labels: performance

#66 - perf: check target locations in sorted order instead of scanning

Pull Request - State: closed - Opened by william-silversmith about 3 years ago - 1 comment
Labels: performance

#65 - perf: use updated dijkstra3d to acquire maxima cheaply

Pull Request - State: closed - Opened by william-silversmith about 3 years ago - 2 comments
Labels: performance

#64 - skeletontricks.find_target scaling issue

Issue - State: closed - Opened by chinasaur about 3 years ago - 21 comments
Labels: performance

#63 - feat: add Command Line Interface

Pull Request - State: closed - Opened by william-silversmith about 3 years ago
Labels: feature

#62 - Obtain Skeleton Result as Numpy Array

Issue - State: closed - Opened by chxii over 3 years ago - 3 comments
Labels: question

#61 - feat: voxel graph support

Pull Request - State: closed - Opened by william-silversmith over 3 years ago - 1 comment
Labels: feature

#60 - Issue with pip installation.

Issue - State: closed - Opened by JacobBumgarner over 3 years ago - 2 comments
Labels: installation

#59 - Command Line Version

Issue - State: closed - Opened by william-silversmith over 3 years ago - 1 comment
Labels: feature

#58 - Fix Borders Doesn't Work on 2D

Issue - State: open - Opened by william-silversmith over 3 years ago
Labels: bug

#57 - Option to Halt postprocessing for Crazy Skeletons

Issue - State: closed - Opened by william-silversmith almost 4 years ago - 1 comment
Labels: feature

#56 - fix(intake): solid color blocks were causing errors

Pull Request - State: closed - Opened by william-silversmith about 4 years ago
Labels: bug

#55 - perf: faster somas

Pull Request - State: closed - Opened by william-silversmith about 4 years ago
Labels: performance

#54 - Question about DAF and PDRF

Issue - State: closed - Opened by jamesnobody about 4 years ago - 2 comments
Labels: question

#53 - What is radius? How to tune scale and const?

Issue - State: closed - Opened by Michaelsqj about 4 years ago - 3 comments
Labels: question

#52 - fix: python3.8 compiles cpp code

Pull Request - State: closed - Opened by william-silversmith over 4 years ago
Labels: installation

#51 - support python3.8?

Issue - State: closed - Opened by jingpengw over 4 years ago - 3 comments
Labels: installation

#50 - feat: add fill_holes argument

Pull Request - State: closed - Opened by william-silversmith over 4 years ago - 4 comments
Labels: feature

#49 - chore: loosen networkx requirement

Pull Request - State: closed - Opened by william-silversmith over 4 years ago
Labels: installation

#48 - Postprocessing Sometimes Slow

Issue - State: closed - Opened by william-silversmith over 4 years ago - 1 comment
Labels: performance

#47 - networkx version

Issue - State: closed - Opened by jingpengw over 4 years ago
Labels: installation

#46 - Hole Protection

Issue - State: closed - Opened by william-silversmith over 4 years ago - 1 comment
Labels: feature

#45 - Compute Cross Sectional Area

Issue - State: open - Opened by william-silversmith over 4 years ago - 2 comments
Labels: feature

#44 - install: compile on windows

Pull Request - State: closed - Opened by william-silversmith over 4 years ago - 1 comment
Labels: installation

#43 - feat: avocado protection (🥑)

Pull Request - State: closed - Opened by william-silversmith over 4 years ago - 6 comments
Labels: feature

#42 - fix: 64-bit addressable _roll_invalidation_cube

Pull Request - State: closed - Opened by william-silversmith over 4 years ago
Labels: bug

#41 - Segmentation Fault

Issue - State: closed - Opened by vkkhare over 4 years ago - 34 comments
Labels: bug

#40 - Avocado Protection (🥑)

Issue - State: closed - Opened by william-silversmith over 4 years ago - 6 comments
Labels: feature

#39 - wip: experimenting with aggressive scaling of astar for PDRF

Pull Request - State: closed - Opened by william-silversmith over 4 years ago - 2 comments
Labels: feature

#38 - perf: implemented flood fill based binary_fill_holes

Pull Request - State: closed - Opened by william-silversmith almost 5 years ago - 4 comments
Labels: performance

#37 - feat: facility for converting synapse centroids into targets

Pull Request - State: closed - Opened by william-silversmith almost 5 years ago
Labels: feature

#36 - same parameters but different result

Issue - State: closed - Opened by chaoyuxie almost 5 years ago - 2 comments
Labels: question

#35 - perf: increase postprocess speed

Pull Request - State: closed - Opened by william-silversmith almost 5 years ago - 2 comments
Labels: performance

#34 - Some examples

Issue - State: closed - Opened by chaoyuxie almost 5 years ago - 3 comments
Labels: question

#33 - feat: specify extra_targets_before and after

Pull Request - State: closed - Opened by william-silversmith almost 5 years ago - 3 comments
Labels: feature

#32 - Reduce Parallel Task Starvation + Better Parallel Progress Bar

Pull Request - State: closed - Opened by william-silversmith about 5 years ago
Labels: feature, performance

#31 - Limit Invalidation to Current Radius Bounded Connected Region

Issue - State: open - Opened by william-silversmith about 5 years ago - 2 comments
Labels: feature

#30 - Skeleton Has Local Hollow for Stochastic Structure

Issue - State: closed - Opened by Hailey-Liu about 5 years ago - 7 comments
Labels: question

#29 - Pictorial Examples

Issue - State: closed - Opened by william-silversmith about 5 years ago - 3 comments
Labels: documentation

#28 - Handle Autapses / Mergers

Issue - State: closed - Opened by william-silversmith about 5 years ago
Labels: feature

#27 - feat: adds join_close_components to postprocess

Pull Request - State: closed - Opened by william-silversmith about 5 years ago - 1 comment
Labels: feature

#26 - perf: ~20x faster unique(label, return_counts=True)

Pull Request - State: closed - Opened by william-silversmith over 5 years ago
Labels: performance

#25 - perf: ~20x faster unique(label, return_counts=True)

Pull Request - State: closed - Opened by william-silversmith over 5 years ago - 1 comment
Labels: performance

#24 - Destroy the Preamble

Issue - State: closed - Opened by william-silversmith over 5 years ago - 4 comments
Labels: performance

#23 - Distribute Segids by Voxel Count for Parallel

Issue - State: closed - Opened by william-silversmith over 5 years ago - 1 comment
Labels: performance

#22 - Task Stealing for Parallel

Issue - State: closed - Opened by william-silversmith over 5 years ago - 1 comment
Labels: performance

#21 - Accept Binary Images

Issue - State: closed - Opened by william-silversmith over 5 years ago
Labels: bug

#20 - perf: faster binary_fill_holes

Pull Request - State: closed - Opened by william-silversmith over 5 years ago
Labels: performance

#19 - Speed up fill_binary_holes

Issue - State: closed - Opened by william-silversmith over 5 years ago - 3 comments
Labels: performance

#18 - Speed Up Dijkstra

Issue - State: closed - Opened by william-silversmith over 5 years ago - 2 comments
Labels: performance

#17 - Trace to Synapses

Issue - State: closed - Opened by william-silversmith over 5 years ago - 1 comment
Labels: feature

#16 - Blood Vessel Detector

Issue - State: open - Opened by william-silversmith over 5 years ago - 1 comment
Labels: feature

#15 - Glia Detector

Issue - State: closed - Opened by william-silversmith over 5 years ago - 3 comments
Labels: feature

#14 - Soma Processing Should Use Border Target Tricks in 3D

Issue - State: closed - Opened by william-silversmith over 5 years ago - 1 comment
Labels: feature

#13 - fix: defend against zero dust threshold

Pull Request - State: closed - Opened by william-silversmith over 5 years ago
Labels: bug

#12 - fix: support anisotropy in border target calculations

Pull Request - State: closed - Opened by william-silversmith over 5 years ago
Labels: bug

#11 - High Anisotropic Ratios Cause Distortions

Issue - State: closed - Opened by william-silversmith over 5 years ago - 3 comments
Labels: bug

#10 - feat: parallel implementation (Cursed Seal Mode)

Pull Request - State: closed - Opened by william-silversmith over 5 years ago
Labels: feature, performance

#9 - feat: add fix_borders parameter & max_paths parameter

Pull Request - State: closed - Opened by william-silversmith over 5 years ago
Labels: feature

#8 - Skeletonize large volumes

Issue - State: closed - Opened by unidesigner over 5 years ago - 22 comments
Labels: question

#7 - fix: accept C order arrays

Pull Request - State: closed - Opened by william-silversmith over 5 years ago
Labels: bug

#6 - Kimimaro Should Accept Fortran and C Arrays

Issue - State: closed - Opened by ghost over 5 years ago - 4 comments
Labels: bug

#5 - Allow specifying root.

Issue - State: open - Opened by william-silversmith over 5 years ago
Labels: feature

#4 - Break Loops

Issue - State: open - Opened by william-silversmith over 5 years ago
Labels: bug

#3 - Parallel Operation

Issue - State: closed - Opened by william-silversmith over 5 years ago - 1 comment
Labels: feature, performance

#2 - Add Testing

Issue - State: open - Opened by william-silversmith over 5 years ago - 1 comment
Labels: testing

#1 - feat: fix branching

Pull Request - State: closed - Opened by william-silversmith over 5 years ago
Labels: feature

GitHub / seung-lab/kimimaro issues and pull requests