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psf-extractor

Characterize the PSF of an optical setup

https://github.com/hoogenboom-group/psf-extractor

Science Score: 44.0%

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    CITATION.cff file
    Found CITATION.cff file
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    Low similarity (6.7%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Characterize the PSF of an optical setup

Basic Info
  • Host: GitHub
  • Owner: hoogenboom-group
  • License: cc-by-4.0
  • Language: Jupyter Notebook
  • Default Branch: master
  • Homepage:
  • Size: 103 MB
Statistics
  • Stars: 8
  • Watchers: 2
  • Forks: 0
  • Open Issues: 3
  • Releases: 0
Created over 4 years ago · Last pushed 8 months ago
Metadata Files
Readme License Citation

README.md

PSF-Extractor

A Python software package to characterize the Point Spread Function of an optical setup.

Created by Daan Boltje, Ernest van der Wee
Made presentable by Ryan Lane
Input from Yoram Vos

Installation

  • Create a new conda environment (assumes Anaconda or Miniconda is already installed) from the terminal $ conda create -n psf -c conda-forge numpy scipy pandas matplotlib scikit-image jupyterlab trackpy xarray cmap

  • Activate environment $ conda activate psf

  • Install directly from github repository (assumes git is installed and in PATH) (psf) $ pip install git+https://github.com/hoogenboom-group/PSF-Extractor.git

To run in a Jupyter notebook

  • (Optional) environment setup for enlightened folk (psf) $ conda install -c conda-forge nodejs (psf) $ pip install tqdm ipympl ipywidgets imagecodecs mpl_interactions

  • Start jupyter lab session (psf) $ cd /path/to/PSF-Extractor/ (psf) $ jupyter lab

  • Run walkthrough.ipynb

Owner

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

Citation (CITATION.cff) 

cff-version: 1.2.0
title: PSF-Extractor
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Daan Benjamin
    family-names: Boltje
    email: d.b.boltje@tudelft.nl
    affiliation: Delft University of Technology
    orcid: 'https://orcid.org/0000-0003-4881-4700'
  - given-names: Ernest Benjamin
    name-particle: van der
    family-names: Wee
    email: E.B.vanderWee@tudelft.nl
    affiliation: Delft University of Technology
    orcid: 'https://orcid.org/0000-0002-0139-4019'
  - 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'
version: 0.1
repository: 'https://github.com/hoogenboom-group/PSF-Extractor'
url: 'https://github.com/hoogenboom-group/PSF-Extractor'
abstract: >-
  A Python software package to characterize the 
  Point Spread Function of an optical setup.
keywords:
  - "point spread function"
  - "optical microscope"
  - software
license: CC-BY-4.0
date-released: '2022-06-01'

GitHub Events

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Dependencies

setup.py pypi