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pims

Python Image Sequence: Load video and sequential images in many formats with a simple, consistent interface.

https://github.com/soft-matter/pims

Science Score: 23.0%

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
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    DOI references
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    Academic publication links
  • ✓
    Committers with academic emails
    13 of 41 committers (31.7%) from academic institutions
  • ○
    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.4%) to scientific vocabulary

Keywords from Contributors

closember qt parallelization ffmpeg pyav notebook gtk tk wx pillow
Last synced: 10 months ago · JSON representation

Repository

Python Image Sequence: Load video and sequential images in many formats with a simple, consistent interface.

Basic Info
Statistics
  • Stars: 266
  • Watchers: 12
  • Forks: 68
  • Open Issues: 79
  • Releases: 10
Created over 12 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

pims: Python Image Sequence

What Problem Does PIMS Solve?

Scientific video can be packaged in various ways: familiar video formats like .AVI and .MOV, folders full of numbered images, or "stacks" of TIFF images. Each of these requires a separate Python module. And, once loaded, they have different methods for accessing individual images, looping through the images in bulk, accessing a specific range, or dealing with multidimensional files. PIMS can do all of these using a consistent interface, handling the differences between different inputs invisibly.

Formats readable by pims include: * Directories or zipfiles of still images (most formats, including TIFF, JPEG, PNG, BMP), and TIFF stacks * Microscope images supported by the Bio-formats project, including Leica, Nikon, Olympus, and Zeiss formats. Requires separate installation; see below. * Movie formats and codecs supported by ffmpeg, including AVI, QuickTime MOV, and H.264 (MP4). May require separate installation; see below. * CINE files from Vision Research cameras * SEQ files from NorPix StreamPix software

PIMS is based on readers by: * scikit-image * ffmpeg and PyAV (video formats such as AVI, MOV) * jpype (interface with Bio-formats) * Pillow (improved TIFF support) * tifffile (alterative TIFF support) * pims_nd2 (improved Nikon .nd2 support) * imageio (a multi-purpose reader package that reads and writes many formats) * moviepy (a Python module that supports video editing) * nd2reader (a Pure Python module for reading Nikon NIS Elements ND2 images and metadata)

Examples & Documentation

Everything is demonstrated in this IPython notebook.

Read the documentation for installation instructions, examples, and further reference.

Core Contributors

  • Daniel Allan founding contributor, slicing and iteration logic, basic readers, display tools
  • Thomas Caswell major refactor, abstract base class
  • Casper van der Wel bioformats readers, display tools
  • Thomas Dimiduk filetype-detecting dispatch logic

Support

This package was developed in part by Daniel Allan, as part of his PhD thesis work on microrheology in Robert L. Leheny's group at Johns Hopkins University in Baltimore, MD. The work was supported by the National Science Foundation under grant number CBET-1033985. Later work was supported by Brookhaven National Lab. Dan can be reached at dallan@bnl.gov.

This package was developed in part by Thomas A Caswell as part of his PhD thesis work in Sidney R Nagel's and Margaret L Gardel's groups at the University of Chicago, Chicago IL. This work was supported in part by NSF Grant DMR-1105145 and NSF-MRSEC DMR-0820054. Later work was supported by Brookhaven National Lab. Tom can be reached at tcaswell@gmail.com.

This package was developed in part by Casper van der Wel, as part of his PhD thesis work in Daniela Kraft's group at the Huygens-Kamerlingh-Onnes laboratory, Institute of Physics, Leiden University, The Netherlands. This work was supported by the Netherlands Organisation for Scientific Research (NWO/OCW).

Owner

  • Name: Soft Matter
  • Login: soft-matter
  • Kind: organization

Code useful for doing soft-matter research

GitHub Events

Total
  • Issues event: 3
  • Watch event: 9
  • Issue comment event: 4
  • Push event: 2
  • Pull request event: 5
  • Fork event: 1
Last Year
  • Issues event: 3
  • Watch event: 9
  • Issue comment event: 4
  • Push event: 2
  • Pull request event: 5
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 764
  • Total Committers: 41
  • Avg Commits per committer: 18.634
  • Development Distribution Score (DDS): 0.656
Past Year
  • Commits: 14
  • Committers: 5
  • Avg Commits per committer: 2.8
  • Development Distribution Score (DDS): 0.643
Top Committers
Name Email Commits
caspervdw c****w@g****m 263
danielballan d****n@g****m 179
Thomas A Caswell t****l@g****m 63
Nathan Keim n****m@c****u 34
baneel b****l@p****u 33
Nathan Keim k****m@p****u 29
Keunhong Park k****r@c****u 17
Genevieve Buckley 3****y@u****m 16
Baptiste n****b@p****u 14
Thomas A Caswell t****l@u****u 12
Antony Lee a****e@g****m 11
BaptisteAN b****l@f****r 11
Ruben Verweij r****n@l****l 9
Lukas Schrangl l****l@t****t 8
Tom Dimiduk t****m@d****t 8
Thomas A Caswell t****l@b****v 7
jthetzel j****l@g****m 6
Hadrien Mary h****y@g****m 5
Charles Reid c****1@g****m 5
Erismena n****s@l****r 4
David Joy v****2@g****m 3
David M. Palmer d****r@g****m 2
John Kirkham k****j@j****g 2
François Boulogne f****g 2
Simon-Martin Schröder m****r@n****e 2
jmoore j****h@g****m 2
Lukas Schrangl s****l@i****t 2
Ruben Verweij v****j@p****l 2
Daniel Firester d****r@D****l 1
Nicholas A. Del Grosso d****k@g****m 1
and 11 more...
Committer Domains (Top 20 + Academic)
princeton.edu: 2 physics.leidenuniv.nl: 2 calpoly.edu: 1 psu.edu: 1 cs.washington.edu: 1 uchicago.edu: 1 free.fr: 1 lighthacking.nl: 1 tuwien.ac.at: 1 dimiduk.net: 1 bnl.gov: 1 live.fr: 1 janelia.hhmi.org: 1 nerdluecht.de: 1 glencoesoftware.com: 1 iap.tuwien.ac.at: 1 arctus.nl: 1 dogcow.cs.washington.edu: 1 sciunto.org: 1 ncsu.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 70
  • Total pull requests: 48
  • Average time to close issues: 8 months
  • Average time to close pull requests: 6 months
  • Total issue authors: 52
  • Total pull request authors: 18
  • Average comments per issue: 1.77
  • Average comments per pull request: 2.67
  • Merged pull requests: 32
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 4
  • Average time to close issues: 7 days
  • Average time to close pull requests: 7 days
  • Issue authors: 3
  • Pull request authors: 2
  • Average comments per issue: 1.0
  • Average comments per pull request: 1.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • nkeim (5)
  • tacaswell (4)
  • bjarthur (3)
  • anntzer (3)
  • GenevieveBuckley (3)
  • danielballan (3)
  • HoseynAAmiri (2)
  • antonkulaga (2)
  • jthetzel (2)
  • WaterKnight1998 (1)
  • kvoit (1)
  • fcakyon (1)
  • ksunden (1)
  • jmdelahanty (1)
  • alexlib (1)
Pull Request Authors
  • anntzer (9)
  • nkeim (8)
  • tacaswell (7)
  • GenevieveBuckley (6)
  • jthetzel (3)
  • danielballan (2)
  • Zethson (2)
  • jstriebel (2)
  • dstansby (2)
  • EitanHemed (2)
  • nickdelgrosso (1)
  • joshmoore (1)
  • dmarx (1)
  • caspervdw (1)
  • Callum-Welsh (1)
Top Labels
Issue Labels
enhancement (5) bug (2) maintenance (1) cleanup (1) documentation (1)
Pull Request Labels
maintenance (2) enhancement (2)

Packages

  • Total packages: 4
  • Total downloads:
    • pypi 71,745 last-month
  • Total docker downloads: 209
  • Total dependent packages: 46
    (may contain duplicates)
  • Total dependent repositories: 220
    (may contain duplicates)
  • Total versions: 42
  • Total maintainers: 4
pypi.org: pims

Python Image Sequence

  • Versions: 23
  • Dependent Packages: 24
  • Dependent Repositories: 200
  • Downloads: 71,745 Last month
  • Docker Downloads: 209
Rankings
Dependent packages count: 0.6%
Downloads: 0.9%
Dependent repos count: 1.1%
Average: 2.4%
Docker downloads count: 2.6%
Stargazers count: 4.0%
Forks count: 5.3%
Maintainers (4)
danielballan Thomas.Caswell caspervdw nkeim
Last synced: 11 months ago
proxy.golang.org: github.com/soft-matter/pims
  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.7%
Dependent repos count: 5.9%
Last synced: 11 months ago
conda-forge.org: pims
  • Versions: 6
  • Dependent Packages: 20
  • Dependent Repositories: 10
Rankings
Dependent packages count: 3.2%
Dependent repos count: 11.1%
Average: 15.2%
Forks count: 22.4%
Stargazers count: 24.3%
Last synced: 11 months ago
anaconda.org: pims
  • Versions: 4
  • Dependent Packages: 2
  • Dependent Repositories: 10
Rankings
Dependent packages count: 20.5%
Average: 32.9%
Forks count: 35.4%
Stargazers count: 37.2%
Dependent repos count: 38.4%
Last synced: 11 months ago

Dependencies

.github/workflows/docs.yaml actions
  • actions/checkout v2 composite
  • peaceiris/actions-gh-pages v3 composite
.github/workflows/tests.yaml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • codecov/codecov-action v1 composite
Dockerfile docker
  • continuumio/miniconda3 latest build
setup.py pypi
  • imageio *
  • numpy >=1.19
  • slicerator >=0.9.8
environment.yml pypi