FrancisCrickInstitute/Etch-a-Cell-Nuclear-Envelope

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Created over 4 years ago
Updated over 4 years ago

FrancisCrickInstitute/Etch-a-Cell-Nuclear-Envelope

FrancisCrickInstitute

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TRACERx-PHLEX

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

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.

Cole_2024

Code associated with Cole et al. 2024

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.