simone-codeluppi Goto Github PK

ipython-in-depth

IPython in-depth Tutorial, first presented at PyCon 2012

ipython_notebooks_public

Ipython notebooks that I created

jupyterlab-configuration

Containerized and Script-controlled JupyterLab Project Environment

jupyterlab_templates

Support for jupyter notebook templates in jupyterlab

karolinska_mlengine

learn-vim

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

mail-importer

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_rcnn

Mask R-CNN for object detection and instance segmentation on Keras and TensorFlow

maskrcnn-benchmark

Fast, modular reference implementation of Instance Segmentation and Object Detection algorithms in PyTorch.

minimal

Minimalist appearance for Emacs

mist

Microscopy Image Stitching Tool for Fiji and standalone

morphsnakes

Morphological snakes for image segmentation and tracking

mpisubmit

MPISubmit - Simple data parallelization using MPI

nd2

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

nd2reader

Simple access to NIS Elements image files.

nuclei_cell_detect

Instance segmentation for nuclei and cells based on facebookresearch maskrcnn benchmark

nucleicuts

An implementation of Al-Kofahi's 2010 paper on nuclear segmentation using graph cutting methods.

opencv

Open Source Computer Vision Library

peaks

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

pelican-bootstrap3

Bootstrap 3 theme for Pelican

phase_correlation

Phase correlation implementation in Python

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)

protocols

My Research Protocols

pycudadecon

Python wrapper for cudaDecon - 3D deconvolution for microscopy

pydata-nyc-2013

Sample iPython notebooks for Image Features in Python talk

pymeanshift

Python Module for Mean Shift Image Segmentation

pysmfish_auto

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

pysmfish_img

Docker file for pysmFISH