Data

Tools

Indexes

Applications

Experiments

Open Source Science

flimview

A software framework to handle, visualize and analyze FLIM data

https://github.com/biophotonics-comi/flimview

Science Score: 33.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    2 of 3 committers (66.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.1%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

A software framework to handle, visualize and analyze FLIM data

Basic Info
  • Host: GitHub
  • Owner: Biophotonics-COMI
  • License: other
  • Language: Jupyter Notebook
  • Default Branch: master
  • Homepage:
  • Size: 70 MB
Statistics
  • Stars: 5
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 6 years ago · Last pushed about 6 years ago

https://github.com/Biophotonics-COMI/flimview/blob/master/ 

## flimview
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3825694.svg)](https://doi.org/10.5281/zenodo.3825694)[![PyPI version](https://badge.fury.io/py/flimview.svg)](https://badge.fury.io/py/flimview)

![fig](figures/viz_sdt.png)


### pip installation

    pip install flimview

### Conda Installation for Jupyter environment

First create a python 3 conda environment

    conda create -n flimview python=3 -y

To activate such environment

    conda activate flimview

To install the need requirements

    conda install -y -c conda-forge jupyterlab ipywidgets nodejs

To enable the widgets

    jupyter labextension install @jupyter-widgets/jupyterlab-manager

and finally to install flimview from github

    pip install flimview --upgrade

#### Optional Packages

To run few things in parallel and other analysis you can install a few more packages

    pip install scikit-image dask[complete] dask-jobqueue --upgrade

### Example data

To get the example data run:

        from flimview import datasets
        # Get SDT example file
        datasets.fetch_sdt()
        # Get PTU file
        datatsets.fetch_ptu()

### Examples

Check the notebooks examples [here](notebooks/)

### Development

To contribute to this package, first clone it:

    git clone https://github.com/Biophotonics-COMI/flimview.git

Then inside flimview

    pip install -e .

Owner

  • Name: Biophotonics Imaging Laboratory - COMI
  • Login: Biophotonics-COMI
  • Kind: organization

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 57
  • Total Committers: 3
  • Avg Commits per committer: 19.0
  • Development Distribution Score (DDS): 0.298
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Matias Carrasco Kind m****d@g****m 40
Matias m****2@i****u 15
Matias Carrasco Kind m****2@i****u 2
Committer Domains (Top 20 + Academic)
iforge.ncsa.illinois.edu: 1 illinois.edu: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 70 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 1
  • Total maintainers: 1
pypi.org: flimview

A software framework to handle, visualize and analyze FLIM data

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 70 Last month
Rankings
Dependent packages count: 10.0%
Dependent repos count: 21.7%
Average: 23.9%
Stargazers count: 25.0%
Forks count: 29.8%
Downloads: 33.0%
Maintainers (1)
mcarrasco
Last synced: 11 months ago

Dependencies

setup.py pypi
  • Pillow *
  • h5py *
  • matplotlib *
  • numpy *
  • pandas *
  • pooch *
  • scipy *
  • sdtfile *
  • tqdm *