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Scientist with a backround in computational biology. Building research tools and reproducible analysis pipelines. Here are some of the projects I've worked on over the years:

Research projects:

Image analysis tools:

  • saibr_fiji_plugin: GUI-based FIJI plugin for performing spectral autofluorescence correction on biological images
  • par-segmentation: Unsupervised ML model for segmenting images of cells and quantifying concentration profiles of membrane proteins
  • matplotlib-polyroi: Simple tool for selecting polygon/spline ROIs on images using matplotlib/Jupyter

Modelling tools:

  • pde-rk: Tool for simulating one-dimensional PDE models with an adaptive Runge-Kutta scheme
  • parameter-space-2d: Tool for performing 2D parameter space analysis for deterministic models using parallel processing

Theses:

  • PhD thesis: Molecular feedback and self-organisation in the PAR polarity network
  • MSci thesis: Computational modelling of Retinotopic Map formation

Tom Bland's Projects

algorithms icon algorithms

Unverified solutions for Tim Roughgarden's Algorithms course on Coursera

andi_challenge icon andi_challenge

Analysis of single particle tracking data for characterisation of anomalous diffusion, using convolutional neural networks. Submitted to the Anomalous Diffusion (AnDi) Challenge

discco icon discco

Quantification of membrane and cytoplasmic concentrations based on differentiable simulation of cell cortex images

healthgps icon healthgps

Global Health Policy Simulation model (Health-GPS)

matplotlib-polyroi icon matplotlib-polyroi

Module for selecting polygonal ROIs on images, spline fitting and ROI expansion

membranequant icon membranequant

Early version of C elegans membrane quantification code (now replaced)

par-segmentation icon par-segmentation

Cell cortex segmentation and quantification in C. elegans PAR protein images

pde-rk icon pde-rk

Functions for simulating one-dimensional PDE models using an adaptive Runge-Kutta scheme

phd-thesis icon phd-thesis

PhD thesis: Molecular feedback and self-organisation in the PAR polarity network

pims icon pims

Python Image Sequence: Load video and sequential images in many formats with a simple, consistent interface.

repo2docker-action icon repo2docker-action

A GitHub action to build data science environment images with repo2docker and push them to registries.

retinotopicmaps icon retinotopicmaps

MSci thesis - modelling the development of neural connections in the visual system

spt icon spt

Single particle tracking using trackpy, diffusion analysis and off-rate analysis

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