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advanced_machine_learning

Code to go along the lecture course "Advanced Machine Learning for Physics, Science, and Artificial Scientific Discovery"

cell-motility-system-for-the-cpm

Ongoing work on cell motility system for the CPM using Morpheus, FitMultiCell, and Python

cell_motility

Simulations for Master Thesis on Statistical Physics of Cell Motility

cell_sorting

Python scripts for Morpheus CPM proyect in Cell Sorting

covidnetwork

Inferring the effect of interventions on COVID-19 transmission networks

facial-similarity-with-siamese-networks-in-pytorch

Implementing Siamese networks with a contrastive loss for similarity learning

first-contributions

🚀✨ Help beginners to contribute to open source projects

fitmulticell_tutorial

Contains code and morpheus files used as a FitMultiCell tutorial for parameter estimation and model selection.

github-slideshow

A robot powered training repository :robot:

it-cert-automation-practice

Google IT Automation with Python Professional Certificate - Practice files

itkelastix-registration

Implementation of the Insight Toolkit's library for whole-slide registration of biological images

machine-learning-for-physicists

Code for "Machine Learning for Physicists 2020" lecture series

machinelearning_r

machinelearninga-z

General working directory for Machine Learning projects.

mcmicro_hackathon_2022

Website for the MCMICRO hackathon 2022

minimal-nextflow-test

Minimal nextflow for workflow for testing and learning

napari

napari: a fast, interactive, multi-dimensional image viewer for python

napari-feature-classifier

napari-spacetx-explorer

A simple plugin for an interactive visualization of spatial omics data.

napari-spatial-omics

napari-spot-detection

practical-python

Practical Python Programming (course by @dabeaz)

pyabc

distributed, likelihood-free inference

scikit-image

Image processing in Python

shell_scripting

Notes and tutorial on shell scripting

spatial-pipeline

Nextflow workflow for the end-to-end analysis image-based spatial-omics data.

spot-detection

starfish

starfish: unified pipelines for image-based transcriptomics

tiny_python_projects

Code for Tiny Python Projects (Manning, 2020, ISBN 1617297518). Learning Python through test-driven development of games and puzzles.

training-resources

Resources for teaching/preparing to teach bioimage analysis