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Sebastian Rhode's Projects

awesome-datascience icon awesome-datascience

:memo: An awesome Data Science repository to learn and apply for real world problems.

bioformatsread icon bioformatsread

This package can be used to read image data using BioFormats into numpy arrays. It was initially created to read CZI image files, but should work with many more image data files thanks to BioFormats.

create_labels_stardist icon create_labels_stardist

script to create labels (for training a deep neural network) based on nucleus segmentation using StarDist (still experimental)

czi_demos icon czi_demos

Collection of scripts and notebooks demostrating how to read and process CZI image files. Still in beta phase ...

czi_playground icon czi_playground

Small python package to simplify reading CZI Image Metadata (*.czi)

czitools icon czitools

This repository provides a collection of tools to simplify reading CZI (Carl Zeiss Image) pixel and metadata in Python. In addition it also contains other useful utilities to visualize CZI images inside Napari.

daskfusion icon daskfusion

Fusing image tiles with dask array's map_blocks

data-science-ipython-notebooks icon data-science-ipython-notebooks

Data science Python notebooks: Deep learning (TensorFlow, Theano, Caffe, Keras), scikit-learn, Kaggle, big data (Spark, Hadoop MapReduce, HDFS), matplotlib, pandas, NumPy, SciPy, Python essentials, AWS, and various command lines.

homemade-machine-learning icon homemade-machine-learning

🤖 Python examples of popular machine learning algorithms with interactive Jupyter demos and math being explained

libczi_sebi06 icon libczi_sebi06

libCZI is an Open Source Cross-Platform C++ library to read and write CZI.

napari-czann-segment icon napari-czann-segment

Semantic Segmention and Image2Image using DeepLearning ONNX models packaged as *.czann files.

oad_sebi06 icon oad_sebi06

Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools and AI tools.

psf_xyz_bead_fit icon psf_xyz_bead_fit

Automatic detection of beads for PSF measurement from Z-Stacks using python-bioformats.

python-scripts icon python-scripts

A repository of python scripts that come in handy in automating day-to-day tasks

python_envs icon python_envs

This repository contains a collection of YML and/or requirments file and tricks to create Python Environments

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