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3d_from_2d

boe_323258

Python code used for micro PIV analysis for the "3D + time blood flow mapping using SPIM-microPIV in the developing zebrafish heart " paper.

clearmap-debug

ClearMap is a python toolbox for the analysis and registration of volumetric data from cleared tissues.

documentation-theme-jekyll

A Jekyll-based theme designed for documentation and help systems. See the link for detailed instructions on setting up and configuring everything.

fisherinformation

Various Matlab code related to photon-statistics / Fisher Information Theory and microscopy

hacklab-training

Training syllabuses for Edinburgh Hacklab

handson-ml

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

image-registration-summer-school-2018

Python notebooks and data for learning about image registration. Hosted at a summer school

image_lddmm_tensorflow

Image mapping using the LDDMM algorithm, implemented in tensorflow

image_overlay_animation

imperialtissuecyte

Resources for tissue imaging at Imperial College London.

openpiv-ipywidget

Jupyter widget GUI for OpenPIV

piv-gui-python

A Qt GUI for inspecting correlation matrices of PIV analysis. This GUI currently uses correlation data format of OpenPIV (www.openpiv.net).

planets

remote_refocus

A scientific publication, describing a way to improve microscopy. This repository hosts everything you need to reproduce our results. Read the publication here: https://amsikking.github.io/remote_refocus/

spadsim

SPAD Simulation

stripe_elimination

MATLAB code from "Eliminating Stripe Artifactsin Light-Sheet Fluorescence Imaging"

swc-hg-novice

Software Carpentry introduction to Mercurial for novices.