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icat-workflow

Post-processing workflow for integrated correlative array tomography (iCAT)

https://github.com/hoogenboom-group/icat-workflow

Science Score: 44.0%

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    Low similarity (6.9%) to scientific vocabulary
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Repository

Post-processing workflow for integrated correlative array tomography (iCAT)

Basic Info
  • Host: GitHub
  • Owner: hoogenboom-group
  • License: cc-by-4.0
  • Language: Jupyter Notebook
  • Default Branch: master
  • Homepage:
  • Size: 116 MB
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 0
  • Open Issues: 3
  • Releases: 1
Created over 7 years ago · Last pushed 8 months ago
Metadata Files
Readme License Citation

README.md

iCAT-workflow

Post-processing workflow for volume CLEM image data.

Installation

Assumes you are logged into a remote Linux server with conda configured.

  1. Vastly overcomplicated but highly recommended environment setup with conda. $ conda create -n icat jupyterlab altair vega_datasets $ conda activate icat $ (icat) conda install -c conda-forge nodejs=15 $ (icat) pip install tqdm lxml ipympl ipywidgets imagecodecs ruamel.yaml $ (icat) pip install git+git://github.com/AllenInstitute/BigFeta/ $ (icat) jupyter labextension install @jupyter-widgets/jupyterlab-manager $ (icat) jupyter labextension install jupyter-matplotlib $ (icat) jupyter nbextension enable --py widgetsnbextension

  2. Install iCAT-workflow from github repo $ (icat) pip install git+https://github.com/hoogenboom-group/iCAT-workflow.git

  3. Clone GitHub repo $ (icat) git clone https://github.com/hoogenboom-group/iCAT-workflow

Getting started

  1. Connect to remote server with port forwarding e.g. ssh -L 8888:localhost:8888 {user}@{server}

  2. (Optional) Download sample data (~3GB) to a convenient location (will take several minutes) $ (icat) cd /path/to/data/storage/ $ (icat) svn export https://github.com/hoogenboom-group/iCAT-data.git/trunk/pancreas

  3. Start jupyter lab session $ (icat) cd ./iCAT-workflow/ $ (icat) jupyter lab --no-browser --port 8888

  4. Open a browser and navigate to http://localhost:8888/lab to run jupyter lab session

Owner

  • Name: hoogenboom-group
  • Login: hoogenboom-group
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
title: "iCAT-workflow"
version: "0.2"
authors:
  - given-names: Ryan
    family-names: Lane
    email: r.i.lane@tudelft.nl
    affiliation: Delft University of Technology
    orcid: https://orcid.org/0000-0002-5887-2069
date-released: 2022-04-15
license: CC-BY-4.0
repository: "https://github.com/hoogenboom-group/CLEMnet"

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Dependencies

setup.py pypi