FrancisCrickInstitute/deep-imcyto FrancisCrickInstitute/deep-imcyto

  • Stars
    star
    1
  • Language
    Python
  • License
    Other
  • Created over 2 years ago
  • Updated 10 months ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
FrancisCrickInstitute/deep-imcyto
github

FrancisCrickInstitute

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

Nextflow pipeline for IMC segmentation tasks.

More Repositories

1

Etch-a-Cell-Nuclear-Envelope

Python
8
star
2

TRACERx-PHLEX

Modular pipeline for integrated analysis of the tumour microenvironment using multiplex imaging
Shell
8
star
3

OmeSliCC

Ome(ro) SLide Image Conversion and Compression pipline (OmeSliCC)
Python
7
star
4

ActiveUnetSegmentation

Unet implementation to work with active contours for segmentations. Using keras and tensorflow 1.15 or 2.5.
Python
5
star
5

cbias-napari

Introduction to Napari training course
Jupyter Notebook
5
star
6

warpAnnotations

A tool to transform annotations (such as points, skeletons or meshes) between spatial datasets.
MATLAB
5
star
7

py-imcyto

IMC segmentation in python.
Jupyter Notebook
4
star
8

napari-tutorial

Modular course teaching the use of napari for image visualisation and analysis
4
star
9

PEACE_melanoma_14_paper

R
3
star
10

babs_uv_polymerase

Simulator of polymerase dynamics during UV damage and repair
Julia
3
star
11

network_borg_blog

Network Borg Blog - Resistance is futile *** Blog Edition - Not Maintained! ***
Python
3
star
12

spherical-phenotype-clustering

Python
2
star
13

Network_Automation_with_Nornir

Network Automation with Nornir
Python
2
star
14

plateplot

Python library for plotting microtitre plates in altair / vega-lite
Python
2
star
15

Making-Lab-Repositories

2
star
16

vanMaldegem_Valand_2021

Code associated with Van Maldegem & Valand et al. 2021, for the analysis of Imaging Mass Cytometry data
R
2
star
17

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
2
star
18

Segment-Flow

Nextflow pipeline for deep learning segmentation models
Python
2
star
19

Spherical_treadmill

C++
1
star
20

mitoem-challenge

Python
1
star
21

TRACERxIMCSpillover

Spillover plugins for TRACERx imaging mass cytometry data analysis, adapted from Chevrier et al 2018.
R
1
star
22

Lattke_et_al_Astrocyte_Maturation

R
1
star
23

DESdemonA

BABS template R script for processing bulk RNASeq data
R
1
star
24

MSTPump

Open source syringe pump
C++
1
star
25

pcr-lambda-test

Python
1
star
26

Electronics-Course-Material

Examples and course material
C++
1
star
27

RAS84_classification

R script to classify lung adenocarcinoma transcriptomes using RAS84 transcriptional signature SVM.
R
1
star
28

Cole_2024

Code associated with Cole et al. 2024
R
1
star
29

StepperController

Controller board for stepper motors
1
star
30

vhl_snRNAseq

Analysis code for VHL tumour snRNAseq datasets from TRACERx renal
R
1
star
31

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.
C++
1
star
32

babs_recruit_2021

Recruitment questions for 2021 vacancy
R
1
star
33

RAS84

Analysis code associated with the development of RAS84, a curated RAS transcriptional signature.
R
1
star
34

Tetrode_plater_breakout_board

1
star
35

network-syslog-summary

Summarise syslog-ng format Cisco logs and graph count. Post results to Slack.
Python
1
star
36

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.
Cuda
1
star