gatoniel
I studied physics at Philipps University Marburg. Currently I am working at Drescher Lab in the field of image analysis and biophysics in the Biozentrum, Basel.
Basel, Switzerland
Pinned Repositories
data-driven-modeling
Julia implementations of Data-Driven Modelling & Scientific Computation, J. Nathan Kutz, Oxford University Press, 2013
geoopt
Riemannian Adaptive Optimization Methods with pytorch optim
good-enough-project
A good enough project template for writing reproducible code
merge-stardist-masks
Merge StarDist Masks - additional postprocessing for StarDist
napari-3d-ortho-viewer
Napari 3D Ortho Viewer - an ortho viewer for napari for 3D images
napari-merge-stardist-masks
Segment non-star-convex objects with StarDist by merging masks.
napari-timeseries-opener-plugin
Simple plugin that opens separate .tif files as a 3-dimensional layer.
podmanspawner
Spawner to use podman with JupyterHub
self-supervised-segmentation
self-supervised segmentation of single species shapes via cycleGAN or differentiable rendering.
gatoniel's Repositories
gatoniel/napari-3d-ortho-viewer
Napari 3D Ortho Viewer - an ortho viewer for napari for 3D images
gatoniel/merge-stardist-masks
Merge StarDist Masks - additional postprocessing for StarDist
gatoniel/geoopt
Riemannian Adaptive Optimization Methods with pytorch optim
gatoniel/good-enough-project
A good enough project template for writing reproducible code
gatoniel/napari-merge-stardist-masks
Segment non-star-convex objects with StarDist by merging masks.
gatoniel/napari-timeseries-opener-plugin
Simple plugin that opens separate .tif files as a 3-dimensional layer.
gatoniel/napari-validate-random-label-predictions
Validate separate instances of label predictions manually
gatoniel/stardist-stacked-timepoints
Combined StarDist segmentation on time stacks.
gatoniel/cookiecutter-napari-plugin
Cookiecutter for napari plugins
gatoniel/dotfiles
dotfiles
gatoniel/credit-mmt-marl
Multi-agent reinforcement learning for credit theory of money and #MMT.
gatoniel/docs
Documentation for napari (other than API docs)
gatoniel/flask
The Python micro framework for building web applications.
gatoniel/gatoniel-utils
Library with utils and helpers for myself.
gatoniel/gatoniel.github.io
gatoniel/jupyterhub
Multi-user server for Jupyter notebooks
gatoniel/napari
napari: a fast, interactive, multi-dimensional image viewer for python
gatoniel/napari-5d-vibrios-viewer
Open separate tif files in napari as n-d file.
gatoniel/napari-grid-cropping
Create multiple crops of an image in a grid like fashion.
gatoniel/napari-nd2-folder-viewer
Look through separate nd2 files in one viewer.
gatoniel/napari-pointslayer-projection
This napari plugin creates a 2d projection of all your points.
gatoniel/napari-segmentation-investigation
Plugin to investigate the differences between a segmentation and the ground truth.
gatoniel/nd2
Full-featured nd2 (Nikon NIS Elements) file reader for python. Outputs to numpy, dask, and xarray. Exhaustive metadata extraction
gatoniel/prospace-pca
A PCA and calculation of means for projective space.
gatoniel/pspca
PCA and calculation of Frechet mean for projective space or sphere.
gatoniel/pytorch-lightning
The lightweight PyTorch wrapper for high-performance AI research. Scale your models, not the boilerplate.
gatoniel/snakemake-slurm-profile
Profile for running snakemake with slurm job submissions
gatoniel/stardist-napari
StarDist plugin for napari
gatoniel/stereographic-link-prediction
A VAE on basis of the kappa-stereographic models from geoopt for link prediction and node classification.
gatoniel/transcription-data-analysis
Analysis of transcription data with VAEs and non-euclidean latent spaces.