JoOkuma
Computer vision engineer at @czbiohub-sf. For cell segmentation & tracking office hours, see link below
Chan Zuckerberg BiohubSF
Pinned Repositories
Huffman_Tree_Compression
Huffman tree compression algorithm written in C, code comments in portuguese
napari
napari: a fast, interactive, multi-dimensional image viewer for python
napari-vector-graphics
grabber
Grabber: A Tool to Improve Convergence in Interactive Image Segmentation
rethinking-interactive-image-segmentation
Implementation of "Rethinking Interactive Image Segmentation: Feature Space Annotation", Pattern Recognition 2022
pyift
PyIFT is a Python wrapper of a fork of the LIDS C library.
dexp
Dataset EXploration & Processing
napari-segment-anything
Segment Anything Model (SAM) native Qt UI
ultrack
Cell tracking and segmentation software
JoOkuma's Repositories
JoOkuma/napari
napari: a fast, interactive, multi-dimensional image viewer for python
JoOkuma/scikit-image
Image processing in Python
JoOkuma/Cassiopeia
A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
JoOkuma/cellcanvas
A tool to support interactive machine learning for cryoET data
JoOkuma/coin-or-cbc-feedstock
A conda-smithy repository for coin-or-cbc.
JoOkuma/coin-or-cgl-feedstock
A conda-smithy repository for coin-or-cgl.
JoOkuma/coin-or-clp-feedstock
A conda-smithy repository for coin-or-clp.
JoOkuma/coin-or-utils-feedstock
A conda-smithy repository for coin-or-utils.
JoOkuma/conda-forge-pinning-feedstock
A conda-smithy repository for conda-forge-pinning.
JoOkuma/Higra
Hierarchical Graph Analysis
JoOkuma/human-eval-bia
Benchmarking Large Language Models for Bio-Image Analysis Code Generation
JoOkuma/jookuma.github.io
My homepage
JoOkuma/mip-feedstock
A conda-smithy repository for mip.
JoOkuma/motile
Multi-Object Tracker using Integer Linear Equations
JoOkuma/nanobind
nanobind: tiny and efficient C++/Python bindings
JoOkuma/napari-animation
A napari plugin for making animations
JoOkuma/napari-convpaint
Segment images by pixel classification based on pre-trained convolutional layer feature extraction
JoOkuma/napari-graph
Efficient graph data structures and algorithms for fast slicing, visualization, and editing
JoOkuma/napari-open-ctc
JoOkuma/napari-spacemouse
JoOkuma/probreg
Python package for point cloud registration using probabilistic model (Coherent Point Drift, GMMReg, SVR, GMMTree, FilterReg, Bayesian CPD)
JoOkuma/py-ctcmetrics
Cell Tracking metrics and tools for the CellTrackingChallenge as described in 'CHOTA: A Higher Order Accuracy Metric for Cell Tracking'
JoOkuma/pyift_rust
JoOkuma/python-mip
Python-MIP: collection of Python tools for the modeling and solution of Mixed-Integer Linear programs
JoOkuma/quarto-scipy24-exercises
JoOkuma/scikit-learn
scikit-learn: machine learning in Python
JoOkuma/segment-anything-2
The repository provides code for running inference with the Meta Segment Anything Model 2 (SAM 2), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.
JoOkuma/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
JoOkuma/traccuracy
Utilities for computing common accuracy metrics on cell tracking challenge solutions with ground truth
JoOkuma/trackastra