simone-codeluppi

amazon-sagemaker-notebook-instance-lifecycle-config-samples

A collection of sample scripts to customize Amazon SageMaker Notebook Instances using Lifecycle Configurations

ashlar

ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration

binary-code-generator

generating A(n, d) codes in python

conda-docker

Create minimal docker images from conda environments

cookiecutter-data-science

A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.

dl-workshop

A deep learning workshop, done from scratch, taught without any frameworks.

elegant-scipy

1st Edition of Elegant SciPy (O'Reilly Publishers)

FISHscale

Spatial analysis of FISH data

gputools

GPU accelerated image/volume processing in Python

gs-quant

Python toolkit for quantitative finance

handson-ml2

A series of Jupyter notebooks that walk you through the fundamentals of Machine Learning and Deep Learning in Python using Scikit-Learn, Keras and TensorFlow 2.

jupyterlab-configuration

Containerized and Script-controlled JupyterLab Project Environment

jupyterlab_templates

Support for jupyter notebook templates in jupyterlab

Learn-Vim

Learning Vim and Vimscript doesn't have to be hard. This is the guide that you're looking for 📖

nd2

Full-featured nd2 (Nikon NIS Elements) file reader for python. With outputs to numpy, dask, and xarray

nuclei_cell_detect

Instance segmentation for nuclei and cells based on facebookresearch maskrcnn benchmark

peaks

A package of utilities for finding, fitting and analyzing punctate image data.

postcode

Decoding of image-based spatial transcriptomics

Probabilistic-Programming-and-Bayesian-Methods-for-Hackers

aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)

probreg

Python package for point cloud registration using probabilistic model (Coherent Point Drift, GMMReg, SVR, GMMTree, FilterReg, Bayesian CPD)

pysmFISH_auto

Version of the pysmFISH pipeline that run without human in the loop

python-storage

SC-cookiecutter-analysis-template

seqfold

pythonic nucleic acid folding

snakemake-workflow-template

A template for standard compliant snakemake-workflows

SpatialViz

Code for "Spatially visualized single-cell pathology of highly multiplexed protein profiles in health and disease"

stardist_pytorch

StarDist PyTorch

storm-analysis

STORM movie analysis code

SuperGluePretrainedNetwork

SuperGlue: Learning Feature Matching with Graph Neural Networks (CVPR 2020, Oral)

ZeroCostDL4Mic

ZeroCostDL4Mic: A Google Colab based no-cost toolbox to explore Deep-Learning in Microscopy