Juan Nunez-Iglesias (@jni)
github

jni

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Top repositories

1

skan

Python module to analyse skeleton (thin object) images
Python
117
star
2

scipy-japan-2019

NumPy tutorial given at SciPy Japan 2019
Jupyter Notebook
33
star
3

ray

Automatic segmentation of electron microscopy volumes
Python
31
star
4

llc-tools

Decorators to make it easier to write SciPy LowLevelCallables
Python
21
star
5

affinder

Quickly find the affine matrix mapping one image to another using manual correspondence points annotation
Python
17
star
6

streaming-talk

Resources for a talk about streaming data analysis in Python
Python
16
star
7

napariboard-proto

Prototype implementation of napari-integrated CNN training viewer
Jupyter Notebook
14
star
8

zarpaint

Paint segmentations directly to on-disk/remote zarr arrays
Python
14
star
9

jax-workshop

Jupyter Notebook
12
star
10

h5cat

Quick preview of HDF5 files on the command line
Python
11
star
11

mysquishy

Recompress zarr chunks in-place
Python
9
star
12

git-tutorial

Notes for a workshop on using git and github
CSS
9
star
13

lma-2021-bioimage-analysis-python

"Bioimage analysis in Python" workshop at LMA2021
Jupyter Notebook
9
star
14

using-python-for-science

The essential guide to using Python for scientists
TeX
7
star
15

functional-programming-in-python

Functional programming in Python talk at Linux Conf Australia 2016
Jupyter Notebook
7
star
16

ipython-config

A config file to keep up with the endless updates from the iPython team.
Python
7
star
17

viridis

A tree library for Python
Python
6
star
18

halfway-to-i2k-skimage-napari

Repo for halfway to i2k workshop: Fundamentals of image analysis in Python with scikit-image, napari, and friends
Python
6
star
19

lesion

Quantify recovery of spinal cord lesions in zebrafish embryos
Python
6
star
20

blob-explorer

Cluster image snippets in an interactive scatterplot and view them
Python
6
star
21

i2k-skimage-napari

Repository for the scikit-image, napari, & friends tutorial at I2K 2020
Jupyter Notebook
5
star
22

mpl-volume-viewer

Simple matplotlib-based volume (3D image) viewer
Jupyter Notebook
5
star
23

pia-tracking

Scripts to work with Pia Larsson's platelet tracking data
Python
4
star
24

napari-midi

Control napari with a USB midi controller
Python
4
star
25

scikit-image-book

Jupyter Notebook
4
star
26

platelet-unet-watershed

Python
4
star
27

skan-talk-scipy-2019

Materials for my talk at SciPy 2019
Jupyter Notebook
4
star
28

aspp2015

Lecture materials for ASPP 2015 in Munich
Jupyter Notebook
3
star
29

sony-digital-paperpile

A synchronisation tool between Paperpile's Google Drive structure and Sony Digital Paper using Box's WebDAV.
Python
3
star
30

fiji-python

Template project to make Python command-line tools to be run by Fiji
Python
2
star
31

numpy-skimage-tutorial

A quick tutorial of NumPy and scikit-image for the COMBINE Python workshop, 2014-11-27
Python
2
star
32

explode-view

Show exploded view of an image.
Python
2
star
33

cellom2tif

Python command line interface to convert Cellomics .C01 files to TIFF.
Python
2
star
34

spectral-graphs

Some tools to do spectral graph analysis in Python
Python
1
star
35

jni.github.io

The home page of Juan Nunez-Iglesias
CSS
1
star
36

performance-tests

A collection of benchmarks to answer Python (initially) performance questions
Python
1
star
37

gel

GEL superpixels: iterative geodesic expansion of labels and recentering
Python
1
star
38

osx-prefs

Command line OSX preferences setup.
Shell
1
star
39

skeletons

Tools to explore skeletonisation methods in 3D
Python
1
star
40

aspp2017-numpy-solutions

Solutions for the NumPy tutorial in ASPP 2017
Jupyter Notebook
1
star
41

aspp-2017-cython-solutions

Solutions for the ASPP 2017 Cython course
Jupyter Notebook
1
star
42

statutes

Statistical utilities
Python
1
star
43

scipy-japan-2020

Repo for SciPy Japan 2020 talk
1
star
44

aspp-2017-cython

Lecture materials for ASPP 2017 in Nikiti, Greece
Jupyter Notebook
1
star
45

betamax

Estimating optimal sampling strategies for high-throughput screens
Python
1
star
46

scientific-programming-in-Python

How to use Python for scientific work
TeX
1
star
47

bashrc

My .bashrc file
Shell
1
star
48

my-documents

A haphazard collection of writing.
1
star
49

skan-scripts

Some scripts and data for skeleton analysis with Python
Python
1
star
50

gaest

Genetic algorithms to clutser expressed sequence tags
C++
1
star
51

synapse-geometry

Examine features of synapse geometry in EM segmentation data
Python
1
star
52

unfold-embryo

Unfold an image along an anterior-posterior axis defined by fluorescence
Python
1
star
53

aspp2017-numpy

Lecture materials for ASPP 2017 in Nikiti, Greece
Jupyter Notebook
1
star