simone codeluppi's Projects
IPython in-depth Tutorial, first presented at PyCon 2012
Ipython notebooks that I created
Containerized and Script-controlled JupyterLab Project Environment
Support for jupyter notebook templates in jupyterlab
Learning Vim and Vimscript doesn't have to be hard. This is the guide that you're looking for 📖
Mail Importer for Gmail will upload the contents of a Thunderbird mail archive to Gmail and do its best to preserve the read state, flagged state, and folders of the messages.
Mask R-CNN for object detection and instance segmentation on Keras and TensorFlow
Fast, modular reference implementation of Instance Segmentation and Object Detection algorithms in PyTorch.
Minimalist appearance for Emacs
Microscopy Image Stitching Tool for Fiji and standalone
Morphological snakes for image segmentation and tracking
MPISubmit - Simple data parallelization using MPI
Full-featured nd2 (Nikon NIS Elements) file reader for python. With outputs to numpy, dask, and xarray
Simple access to NIS Elements image files.
Instance segmentation for nuclei and cells based on facebookresearch maskrcnn benchmark
An implementation of Al-Kofahi's 2010 paper on nuclear segmentation using graph cutting methods.
Open Source Computer Vision Library
A package of utilities for finding, fitting and analyzing punctate image data.
Bootstrap 3 theme for Pelican
Phase correlation implementation in Python
Decoding of image-based spatial transcriptomics
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 ;)
Python package for point cloud registration using probabilistic model (Coherent Point Drift, GMMReg, SVR, GMMTree, FilterReg, Bayesian CPD)
My Research Protocols
Python wrapper for cudaDecon - 3D deconvolution for microscopy
Sample iPython notebooks for Image Features in Python talk
Python Module for Mean Shift Image Segmentation
Version of the pysmFISH pipeline that run without human in the loop
Docker file for pysmFISH