Pinned Repositories
3D-Cell-Nuclei-Denoising-and-Segmentation
A novel generic dictionary-based denoising method for improving noisy and densely packed nuclei segmentation in 3D time-lapse fluorescence microscopy images
ACEnet-for-Neuroanatomy-Segmentation
ACEnet: Anatomical Context-Encoding Network for Neuroanatomy Segmentation
AnyStar
[WACV 2024] Reference implementation of "AnyStar: Domain randomized universal star-convex 3D instance segmentation"
awesome-tda
A curated list of topological data analysis (TDA) resources and links.
Betti-matching
blob-detector
LoG blob detection
Brain-ID
Learning Contrast-agnostic Anatomical Representations for Brain Imaging
bv3dbox-segment-good
The known BioVoxxel Toolbox functions now improved for 2D and 3D images
consistency-ranking-loss
The code for ICLR2023: Confidence Estimation Using Unlabeled Data
Dijkstra-s-shortest-path-algorithm
Using binary heaps, binomial heaps, and fibonacci heaps
ckadipas's Repositories
ckadipas/ACEnet-for-Neuroanatomy-Segmentation
ACEnet: Anatomical Context-Encoding Network for Neuroanatomy Segmentation
ckadipas/AnyStar
[WACV 2024] Reference implementation of "AnyStar: Domain randomized universal star-convex 3D instance segmentation"
ckadipas/awesome-tda
A curated list of topological data analysis (TDA) resources and links.
ckadipas/Betti-matching
ckadipas/blob-detector
LoG blob detection
ckadipas/Brain-ID
Learning Contrast-agnostic Anatomical Representations for Brain Imaging
ckadipas/bv3dbox-segment-good
The known BioVoxxel Toolbox functions now improved for 2D and 3D images
ckadipas/consistency-ranking-loss
The code for ICLR2023: Confidence Estimation Using Unlabeled Data
ckadipas/DMT_loss
DMT codes for the ICLR 2021 paper: Topology-Aware Segmentation Using Discrete Morse Theory
ckadipas/euclidean-distance-transform-3d
Euclidean distance & signed distance transform for multi-label 3D anisotropic images using marching parabolas.
ckadipas/Limbic_Thalamus
ckadipas/QuanTAV
Novel Radiomic Measurements of Tumor-Associated Vasculature Morphology on Clinical Imaging as a Biomarker of Treatment Response in Multiple Cancers
ckadipas/hsynex
A tool for hypothalamus subregion segmentation capable of working across different MRI modalities and resolution
ckadipas/JUMP
ckadipas/MedSAM
Segment Anything in Medical Images
ckadipas/MeshFix-V2.1
Converts a raw digitized polygon mesh to a clean mesh where all the occurrences of a specific set of "defects" are corrected. Holes, self-intersections, degenerate and non-manifold elements are all replaced with valid configurations.
ckadipas/nii2mesh
Convert NIfTI volume to triangulated mesh using marching cubes
ckadipas/niimath
niimath - a clone of fslmaths. Try the live demo:
ckadipas/niivue
a WebGL2 based medical image viewer. Supports over 30 formats of volumes and meshes.
ckadipas/Path2MR
This a 3D histology reconstruction pipeline that can be implemented with sparse histological sampling and in absence of an MRI reference. This repository described steps of the pipeline and provides access to code for its implementation.
ckadipas/PEPSI
[MICCAI 2024] PEPSI: Pathology-Enhanced Pulse-Sequence-Invariant Representations for Brain MRI
ckadipas/SEEG4D
ckadipas/SpatialCorrection
Learning to Segment from Noisy Annotations: A Spatial Correction Approach
ckadipas/struct-uncertainty
This repository contains the implementation for our work "Topology-Aware Uncertainty for Image Segmentation", accepted to NeurIPS 2023.
ckadipas/Structural_Uncertainty
Codes for 'Learning Probabilistic Structural Representation for Biomedical Image Segmentation'
ckadipas/surf-ice
GLSL surface rendering source code. Compiled versions available from NITRC. Loads 3DS, CTM, DXF, FreeSurfer, GII (GIfTI), GTS, LWO2, MS3D, MZ3, NV (BrainNetViewer), OBJ, OFF, PLY, STL, VTK. Tractography formats include BFloat, PDB, TCK, TRK, and VTK. Also NIfTI format voxelwise images.
ckadipas/SynthSeg
Contrast-agnostic segmentation of MRI scans
ckadipas/thomas_new
Segmentation of the thalamus into 11 nuclei and MTT using white-matter-nulled MPRAGE MRI image contrast with support now for standard MPRAGE also (Version 2.1) © Copyright Manojkumar Saranathan 2021 2022
ckadipas/topofit
Rapid, topologically-correct cortical surface reconstruction
ckadipas/TopoLoss
Code for the NeurIPS 2019 paper: Topology-Preserving Deep Image Segmentation