constantinpape/dl-teaching-resources

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constantinpape/dl-teaching-resources

constantinpape

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Collection of teaching material for deep learning for (biomedical) image analysis

z5

Lightweight C++ and Python interface for datasets in zarr and N5 format

torch-em

Deep-learning based semantic and instance segmentation for 3D Electron Microscopy and other bioimage analysis problems based on pytorch.

elf

Utils and convenience functions for large-scale bio-image analysis.

cluster_tools

Distributed segmentation for bio-image-analysis

heimdall

Python based viewer for large mulit-dimensional datasets.

pybdv

python tools for BigDataViewer

affogato

Affinity based segmentation algorithms and tools

Jupyter Notebook

training-deep-learning-models-for-vison

Jupyter Notebook

rf_benchmarks

Benchmarking Random Forests for ilastik.

machine_learning

Repo for machine learning project.

cremi_tools

3d-unet-benchmarks

dalle-mini-poster

Create posters from dalle-mini / craiyon screenshots

skeletor

Tools and wrappers for skeletonization.

skanner

Tools for skeleton analysis with skan

deep-micro-val

Evaluating segmentation methods for common cell segmentation problems

z5py-benchmarks

ASV benchmark suite for z5 / z5py

DenseReconstruction

mutex-watershed

The mutex watershed for image segmentation

pyopengm

Modern python wrapper for opengm

stuff_master

Misc. programed during master / neuro segmentation

boots

out of the box segmentation

gpu_benchmarks

pyaffine

Affine transformations in python (prototype)

quantile_tests

Comparing calculation of quantiles with boost and vigra accumulators

minitorch

Lightweight torch wrapper for bio-medical segmentation

paintera_tools

Tools for generating, curating and merging paintera datasets