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Kreshuk Group - Machine learning for bioimage analysis

3d-gt-tools

List of tools for creating ground truth annotations for 3D data

bioimg_rs

A rust implementation of bioimage spec parser

centriole_detection

drosophila_embryo_cells

Drosophila emryo cell classification

embl-deep-learning-course-2023-

EMBL Deep Learning course 2023 exercises and materials

embryo_stage_classifier

Model for classifying drosophila embryo stages

go-nuclear

Guides and code for 3D nuclear instance segmentation

gpu_envs

Setting up mixed conda and easybuild environments on the EMBL cluster

hiiragi_segmentation_cluster_tools

hylfm-net

kinetochores_segmentation

kreshuklab-utils

Python package for common lab code

learning-temporal-consistency

morphofeatures

MorphoFeatures code and data

mouse-embryo-seg

3D segmentation of nuclei (fixed) and cells (live) of the developing mouse embryo

neuroclear

Neuroclear is a deep-learning-based Python module to train a deep neural network for the task of applying super-resolution to degraded axial resolution in fluorescence microscopy, using a single image stack.

plant-seg

A tool for cell instance aware segmentation in densely packed 3D volumetric images

plantseg-cellpose-augmentation

predoc-course

Kreshuk Lab's EMBL EIPP predoc course teaching material, each branch keeps the record of a specific season

protozoo

rewardchecking

Checking reward functions for lines and circles with line and circle data.

rlforseg

sea-urchin-em-segmentation

shallow2deep

Shallow2deep: Exploiting feature-based classifiers for domain adaptation in semantic segmentation

spoco

PyTorch implementation of SPOCO

summer

deep learning project for summer school

takafumi_embryos_segmentation

teaching-dl-course-2019

EMBL Deep Learning course 2019 exercises and materials

teaching-dl-course-2020

EMBL Deep Learning course 2020-21 exercises and materials