Martin Fitzpatrick (Page 2)

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Python Dictionaries

A rather long guide to Python's key:value lookup type

Driving I2C OLED displays with MicroPython

Driving I2C monochrome displays with SSD1306 from MicroPython

Turning a Lucky Cat into a Persistence of Vision display

Turning a Lucky Cat into a Persistence of Vision display

Python-powered Maneki-neko persistence of vision scroller

Wemos D1 pin numbers & functions

Pin mapping and I2C/SPI from MicroPython

Building a MicroPython heart rate monitor

Building a MicroPython heart rate monitor

Finding the beat in HR sensor data

Heart rate sensors

Photoplethysmography, because that's a real word

KropBot

The multiplayer internet-controlled robot. It turns out it's a terrible idea.

Scroll pHAT Tetris

The Scroll pHAT is a little 11x5 (55) white LED matrix pHAT which you can control easily from a Raspberry Pi. In this project we'll squeeze a tiny-yet-playable game of Tetris onto the Scroll pHAT. https://blog.martinfitzpatrick.com/static/video/scroll-phat-tetris-play.mp4 RequirementsRaspberry Pi Zero / Zero W

Partial Least Squares Discriminant Analysis (PLS-DA) with Python

Partial least squares discriminant analysis (PLS-DA) is an adaptation of PLS regression methods to the problem of supervised clustering. It has seen extensive use in the analysis of multivariate datasets, such as that derived from NMR-based metabolomics. In this method the groups within the samples are already known (e.g.

1D 1H NMR data processing

1D 1H NMR data processing

1D 1H NMR is a commonly applied to metabolomic studies, being well suited to untargeted analysis of complex biofluids. It has been successfully applied to the classification and diagnosis of a number of diseases including [ref]. There are a number of important steps that must be applied prior 1D 1H

Wooey

Simple, automated web UIs for Python scripts

Getting Started with Pathomx

This is quick start-up guide for new users of Pathomx. Following it should give you everything that you need to know to start using Pathomx right away. Pathomx aims to offer a powerful, extensible analysis and processing platform while being as simple to use as possible to the casual user.

Gremlins in the Machine

Creating custom tools for the Pathomx data analysis platform

PyQt5 support in Matplotlib

My pull-request for matplotlib to add PyQt5 support has been accepted and merged, meaning PyQt5 support will be available in the upcoming v1.4.0 release of matplotlib. Based off original work by @badders this re-implements the Qt backend structure as Qt5-first, with Qt4 wrappers for compatibility. It's

Automatic phase correction of NMR spectra

This notebook demonstrates automatic phase correction algorithms implemented for nmrglue. Two standard algorithms are implemented: * ACME algorithm by Chen Li et al. Journal of Magnetic Resonance 158 (2002) 164-168 * Naive peak minima minimisation The outputs for the two algorithms are shown below. Automatic phase correction can be used through the

NMRLab 1D NMR processing (MATLAB)

This notebook uses a subset of the available processing features in NMRLab (+Metabolab) to process 1D NMR spectra. The output is saved as a CSV file that can be imported into pandas, PLS_Toolbox or any other package for subsequent analysis. To use this workbook you will need an installation

Snippets (MATLAB)

This notebook contains snippets of code that are useful when working with MATLAB in IPython Notebooks.

MetaboHunter 1D NMR Identification (Python Interface) Demo

MetaboHunter is a web service for automated assignment of 1D raw, bucketed or peak picked NMR spectra. Identification is performed in comparison to two publicly available databases (HMDB, MMCD) of NMR standard measurements. More information about the algorithm is available in the published paper: 📙Tulpan, D., Leger, S., Belliveau, L.

MetaboHunter Interface

1D NMR Metabolite Identification from Python

BioCyc (API)

Python interface to the BioCyc Web API

BioCyc Interface Demo

This notebook is a quick demo of a BioCyc Web API I've released for Python. While incomplete the API offers access to most basic attributes for metabolites, proteins, reactions, pathways and organisms in the database. The Python interface comes with an disk-based caching mechanism under ~/.biocyc that greatly

Measuring cell fluorescence using ImageJ

Determining the level of cellular fluorescence from fluorescence microscopy images in ImageJ

Dot Blot Analysis with ImageJ

Analyzing a dot blot in ImageJ by background subtraction and measuring the integrated density of each dot. This dot blot image is available in the File/Open Samples menu in ImageJ 1.33s or later. This method usually requires background correction of the image, which can be done using the

QtIPy

QtIPy — The data automator!

mplstyler

A simple API to keep line and marker styles consistent throughout plots