Data

Tools

Indexes

Applications

Experiments

Open Source Science

pyimzml

A parser to read .imzML files with python

https://github.com/alexandrovteam/pyimzml

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
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: pubmed.ncbi, ncbi.nlm.nih.gov
  • ✓
    Committers with academic emails
    7 of 14 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.7%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

A parser to read .imzML files with python

Basic Info
  • Host: GitHub
  • Owner: alexandrovteam
  • License: apache-2.0
  • Language: Python
  • Default Branch: master
  • Size: 443 KB
Statistics
  • Stars: 41
  • Watchers: 10
  • Forks: 20
  • Open Issues: 3
  • Releases: 0
Created over 11 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.rst 

pyimzML
=======

.. image:: https://readthedocs.org/projects/pyimzml/badge/?version=latest
    :target: http://pyimzml.readthedocs.org/en/latest/?badge=latest
    :alt: Documentation Status

Description
-----------
A parser for the imzML format used in imaging mass spectrometry. See specification
`here  `_.
Designed for use with imzML version 1.1.0. Outputs data as python lists and dicts.

The parser is developed by `Alexandrov Team `_ at EMBL Heidelberg.

Installation
------------
pyimzML is available on `PyPI `_. pyimzML
should be installed with pip using one of these three options:

* ``$ pip install pyimzml`` will install pyimzML from PyPI (easiest).
* ``$ pip install git+git://github.com/alexandrovteam/pyimzML.git`` will install pyimzML from github.
* Download the source tarball from `PyPI `_ and ``$ pip install pyimzml-x-x-x.tar.gz``

**Dependency Notes**

* pyimzML has an optional dependency to `lxml `_. If lxml is not installed, pyimzML will instead use the built-in cElementTree or ElementTree package.

**Testing**

To test your installation of pyimzML, you can download sample data from `imzml.org `_ and run the tests.

Attribution
-----------

The pyimzml/ontology directory includes data derived from the following ontologies:

* `Units of measurement ontology `_ by George Gkoutos `CC-BY license `_
* `Mass spectrometry ontology `_ by `Gerhard Mayer et al. `_ `CC-BY license `_
* `Imaging MS controlled vocabulary `_

Documentation
-------------

Documentation is available on `ReadTheDocs `_

Owner

  • Name: Tools developed by Alexandrov Team, EMBL
  • Login: alexandrovteam
  • Kind: organization
  • Location: Heidelberg, Germany

Mainly for processing and analysis of mass spectrometry and imaging MS data

GitHub Events

Total
  • Watch event: 8
  • Delete event: 1
  • Push event: 2
  • Pull request event: 1
  • Fork event: 3
Last Year
  • Watch event: 8
  • Delete event: 1
  • Push event: 2
  • Pull request event: 1
  • Fork event: 3

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 105
  • Total Committers: 14
  • Avg Commits per committer: 7.5
  • Development Distribution Score (DDS): 0.724
Past Year
  • Commits: 2
  • Committers: 1
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Dominik Fay d****y@g****e 29
andy-d-palmer p****r@e****e 18
Jonathan Brauer j****r@g****m 14
Lachlan Stuart 2****t 13
Dominik Fay d****y@e****e 10
Sergii Mamedov f****a@g****m 4
Artem Tarasov a****v@e****e 4
Theodore A t****a@g****m 4
Vitaly Kovalev k****v@e****e 3
Vitaly Kovalev v****v@e****e 2
andydpalmer p****h@g****m 1
Paolo Inglese p****4@i****k 1
Vitaly Kovalev 1****o 1
andy-d-palmer a****r@e****e 1
Committer Domains (Top 20 + Academic)
embl.de: 6 imperial.ac.uk: 1 gmx.de: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 14
  • Total pull requests: 30
  • Average time to close issues: over 1 year
  • Average time to close pull requests: about 2 months
  • Total issue authors: 11
  • Total pull request authors: 9
  • Average comments per issue: 2.79
  • Average comments per pull request: 0.43
  • Merged pull requests: 25
  • 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
  • leorrose (2)
  • paoloinglese (2)
  • andy-d-palmer (2)
  • aryre (1)
  • hanghu1024 (1)
  • hzxxxxxx (1)
  • Kawue (1)
  • Kumarsan201006 (1)
  • krishnakantsingh14 (1)
  • inaciomdrs (1)
  • DinosaurInSpace (1)
Pull Request Authors
  • sergii-mamedov (12)
  • andy-d-palmer (6)
  • LachlanStuart (5)
  • jonathanimb (3)
  • intsco (3)
  • ZhengnanCheng (2)
  • paoloinglese (2)
  • leorrose (1)
  • gtluu (1)
Top Labels
Issue Labels
bug (2) question (1) help wanted (1)
Pull Request Labels
bug (4) enhancement (4)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 2,889 last-month
  • Total dependent packages: 6
  • Total dependent repositories: 10
  • Total versions: 19
  • Total maintainers: 1
pypi.org: pyimzml

Parser for conversion of imzML 1.1.0 files

  • Versions: 19
  • Dependent Packages: 6
  • Dependent Repositories: 10
  • Downloads: 2,889 Last month
Rankings
Dependent packages count: 1.4%
Dependent repos count: 4.6%
Average: 6.9%
Downloads: 7.6%
Forks count: 8.9%
Stargazers count: 11.8%
Maintainers (1)
alexandrov_team
Last synced: 11 months ago

Dependencies

docs/requirements.txt pypi
  • numpy >=1.10
  • sphinx-rtd-theme ==0.5.0
  • sphinx_autodoc_typehints *
  • wheezy.template *
setup.py pypi
  • numpy *
  • wheezy.template *
.github/workflows/pythonpublish.yml actions
  • actions/checkout v1 composite
  • actions/setup-python v1 composite