lukmuk
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Distributed segmentation for bio-image-analysis
Everything about note management. All in Zotero.
Semi automated image analysis toolkit for Connectomics
A template repo used to make new napari plugins
Automated data collection for the TriBeam microscope
transparent proxy server for llama.cpp's server to provide automatic model swapping
A toolbox for registering / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.
Zarr core protocol for storage and retrieval of N-dimensional typed arrays
3D Slicer extension for Segment Anything Model (SAM) developed by Meta
HIP: C++ Heterogeneous-Compute Interface for Portability
Fiji plugins for the creation of binary and semantic masks from ROIs in the RoiManager. Works with stacks too.
Convert stacks of images to chunked datasets
A program interfacing Segment Anything with cryoSPARC via cryosparc-tools to efficiently identify vesicle-embedded membrane proteins and complexes in cryo-EM micrographs.
Denoise event-based camera data based on correlation.
Data acquisition scripts for FIBSEM
Preprocess a FIB/SEM-Stack using Fiji from "Auto Slice & View" by Thermofischer Scientific
Deep learning segmentation for 3D FIB-SEM data of porous cathode materials using fused image inputs.
Particle Accelerator and FEL Beam Simulation Codes: elegant, EPICS, JSPEC, OPAL, Radia, Shadow3, SRW, Synergia, Warp, Zgoubi
Image Restoration Toolbox (PyTorch). Training and testing codes for DPIR, USRNet, DnCNN, FFDNet, SRMD, DPSR, BSRGAN, SwinIR
Flood-Filling Networks for instance segmentation in 3d volumes.
Python implementation of the Fourier Ring Correlation (FRC) to determine image resolution
Optical flow - driven volumetric (3D) Gaussian denoising
Inputs a MRC file, an interpolation factor (2, 4, ...) and an axis (X, Y or Z), and outputs an interpolated MRC file.