FrancisCrickInstitute/Cole_2024

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Created 8 months ago
Updated 8 months ago

FrancisCrickInstitute/Cole_2024

FrancisCrickInstitute

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Code associated with Cole et al. 2024

TRACERx-PHLEX

Modular pipeline for integrated analysis of the tumour microenvironment using multiplex imaging

Etch-a-Cell-Nuclear-Envelope

OmeSliCC

Ome(ro) SLide Image Conversion and Compression pipline (OmeSliCC)

ActiveUnetSegmentation

Unet implementation to work with active contours for segmentations. Using keras and tensorflow 1.15 or 2.5.

cbias-napari

Introduction to Napari training course

Jupyter Notebook

warpAnnotations

A tool to transform annotations (such as points, skeletons or meshes) between spatial datasets.

sparks

Jupyter Notebook

py-imcyto

IMC segmentation in python.

Jupyter Notebook

napari-tutorial

Modular course teaching the use of napari for image visualisation and analysis

PEACE_melanoma_14_paper

babs_uv_polymerase

Simulator of polymerase dynamics during UV damage and repair

network_borg_blog

Network Borg Blog - Resistance is futile *** Blog Edition - Not Maintained! ***

image-analysis-outreach

A collection of materials and information for school outreach sessions about image analysis

IonVisualise

spherical-phenotype-clustering

Network_Automation_with_Nornir

Network Automation with Nornir

plateplot

Python library for plotting microtitre plates in altair / vega-lite

Making-Lab-Repositories

RAS84

Analysis code associated with the development of RAS84, a curated RAS transcriptional signature.

vanMaldegem_Valand_2021

Code associated with Van Maldegem & Valand et al. 2021, for the analysis of Imaging Mass Cytometry data

protocolBLAST

Sample preparation and warping accuracy for correlative multimodal imaging in the mouse olfactory bulb using two-photon, synchrotron X-ray and volume electron microscopy

Jupyter Notebook

Segment-Flow

Nextflow pipeline for deep learning segmentation models

multi-dimensional-imaging-and-analysis

Jupyter Notebook

deep-imcyto

Nextflow pipeline for IMC segmentation tasks.

tumour-growth-patterns-impact-evolution

Agent-based modelling reveals the impact of growth patterns on spatial and temporal features of clonal diversification. A GitHub repository of the Source Code for the model and Source Data for the figures of the paper.

babs-pre-quarto

Pre-processor to produce parametrised Quarto websites

dm3d-pages

Deforming mesh 3D usage.

Spherical_treadmill

mitoem-challenge

TRACERxIMCSpillover

Spillover plugins for TRACERx imaging mass cytometry data analysis, adapted from Chevrier et al 2018.

Lattke_et_al_Astrocyte_Maturation

DESdemonA

BABS template R script for processing bulk RNASeq data

MSTPump

Open source syringe pump

pcr-lambda-test

Electronics-Course-Material

Examples and course material

RAS84_classification

R script to classify lung adenocarcinoma transcriptomes using RAS84 transcriptional signature SVM.

StepperController

Controller board for stepper motors

vhl_snRNAseq

Analysis code for VHL tumour snRNAseq datasets from TRACERx renal

4-Stepper-motor-control-board

Board to control 4 stepper motors based on the Teesny 3.5 dev. board. It has a small OLED display and 4 rotary encoders with switch and 2 DAC outputs in BNC connectors.

babs_recruit_2021

Recruitment questions for 2021 vacancy

Tetrode_plater_breakout_board

CALM

Crick Advanced Light Microscopy

Jupyter Notebook

network-syslog-summary

Summarise syslog-ng format Cisco logs and graph count. Post results to Slack.