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generate-tiff-offsets

Generate tiff offsets for optimized remote viewing

https://github.com/hms-dbmi/generate-tiff-offsets

Science Score: 75.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: nature.com
  • ○
    Academic email domains
  • ✓
    Institutional organization owner
    Organization hms-dbmi has institutional domain (dbmi.hms.harvard.edu)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.7%) to scientific vocabulary

Keywords

hidivelab
Last synced: 6 months ago · JSON representation ·

Repository

Generate tiff offsets for optimized remote viewing

Basic Info
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 4
  • Open Issues: 2
  • Releases: 2
Topics
hidivelab
Created over 5 years ago · Last pushed about 1 year ago
Metadata Files
Readme License Citation

README.md

generate-tiff-offsets

A python cli (and web-application) for generating an Image File Directory (IFD) index for TIFFs. See the benchmark from our paper or watch our video explainer to learn more about how our strategy improves random chunk access speeds for OME-TIFF in Viv.

TIFF IFD Index specification

The content of an TIFF IFD Index should match the given description here.

Version 0

Prototype spec for the structure required for TIFF IFD Index (JSON):

[IFD_offset_0, IFD_offset_1, IFD_offset_2, IFD_offset_3, ..., IFD_offset_N]

where IFD_offset_n corresponds to the nth byte-offset for the corresponding Image File Directory in the linear TIFF series.

Note For OME-TIFF, the ordering of IFDs is determined by the DimensionOrder attribute in the OME-XML metadata. Each combination of C, Z, and T corresponds to one IFD, meaning the total number of IFDs is the product of these dimensions (T x C x Z) and independent of the number of pyramidal resolutions in the OME-TIFF.

🐍 Python CLI

bash pip install generate-tiff-offsets generate_tiff_offsets --input_file <my_file>.ome.tiff

This command writes the Version 0 Index to the local file system, adjacent to the input TIFF with the file name <my_file>.offsets.json.

Warning Our OME-TIFF web-viewer, Avivator expects this naming convension and folder structure in order for the Indexed OME-TIFF to be recognized.

🌎 Web application

The website requires no installation and can be used to generate the Version 0 index directly in the browser. See our video tutorial for usage instructions.

Owner

  • Name: Harvard Medical School - Department of Biomedical Informatics
  • Login: hms-dbmi
  • Kind: organization
  • Location: Boston

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it using these metadata."
authors:
  - given-names: "Ilan"
    family-names: "Gold"
    affiliation: "Harvard Medical School"
  - given-names: "Trevor"
    family-names: "Manz"
    affiliation: "Harvard Medical School"
title: "Indexed OME-TIFF CLI"
url: "https://github.com/hms-dbmi/generate-tiff-offsets"
preferred-citation:
  type: article
  title: "Viv: multiscale visualization of high-resolution multiplexed bioimaging data on the web"
  authors:
    - given-names: "Trevor"
      family-names: "Manz"
      orcid: "https://orcid.org/0000-0001-7694-5164"
      affiliation: "Harvard Medical School"
    - given-names: "Ilan"
      family-names: "Gold"
      orcid: "https://orcid.org/0000-0002-5823-1026"
      affiliation: "Harvard Medical School"
    - given-names: "Nathan Heath"
      family-names: "Patterson"
      affiliation: "Vanderbilt University"
      orcid: "https://orcid.org/0000-0002-0064-1583"
    - given-names: "Chuck"
      family-names: "McCallum"
      affiliation: "Harvard Medical School"
      orcid: "https://orcid.org/0000-0003-4039-9768"
    - given-names: "Mark S."
      family-names: "Keller"
      affiliation: "Harvard Medical School"
      orcid: "https://orcid.org/0000-0003-3003-874X"
    - given-names: "Bruce W."
      family-names: "Herr"
      name-suffix: "II"
      affiliation: "Indiana University"
      orcid: "https://orcid.org/0000-0002-6703-7647"
    - given-names: "Kay"
      family-names: "Börner"
      affiliation: "Indiana University"
      orcid: "https://orcid.org/0000-0002-3321-6137"
    - given-names: "Jeffrey M."
      family-names: "Spraggins"
      affiliation: "Vanderbilt University"
      orcid: "https://orcid.org/0000-0001-9198-5498"
    - given-names: "Nils"
      family-names: "Gehlenborg"
      affiliation: "Harvard Medical School"
      orcid: "https://orcid.org/0000-0003-0327-8297"
  doi: "10.1038/s41592-022-01482-7"
  journal: "Nature Methods"
  month: 5
  year: 2022

GitHub Events

Total
  • Create event: 4
  • Issues event: 2
  • Release event: 3
  • Watch event: 1
  • Delete event: 2
  • Issue comment event: 1
  • Push event: 11
  • Pull request event: 2
Last Year
  • Create event: 4
  • Issues event: 2
  • Release event: 3
  • Watch event: 1
  • Delete event: 2
  • Issue comment event: 1
  • Push event: 11
  • Pull request event: 2

Dependencies

.github/workflows/publish.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • pypa/gh-action-pypi-publish release/v1 composite
.github/workflows/test.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v5 composite
  • astral-sh/setup-uv v3 composite
pyproject.toml pypi
  • tifffile >=2023.9.26