Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/alleninstitute/merquaco

https://github.com/alleninstitute/merquaco

Science Score: 36.0%

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
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.7%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: AllenInstitute
  • License: other
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 68.4 MB
Statistics
  • Stars: 7
  • Watchers: 1
  • Forks: 3
  • Open Issues: 4
  • Releases: 0
Created about 2 years ago · Last pushed 11 months ago
Metadata Files
Readme License

README.rst 

MERQuaCo
========

**MERQuaCo** is a tool for assessing the quality of spatial transcriptomics experiments on the Vizgen MERSCOPE platform. **MERQuaCo** computes a range of metrics to assess transcript detection efficiency in space, tissue integrity, and data loss using the transcripts table, codebook, and DAPI image. All analyses ignore cell segmentation boundaries and only use information pertaining to transcript locations.

Installation
------------

.. code-block:: bash

    $ git clone https://github.com/AllenInstitute/merquaco.git
    $ cd merquaco
    $ pip install .

Usage
-----
Refer to the `demo notebook `_ and `documentation `_ for example usage

Manuscript
---------- 
Refer to our manuscript `Martin, Olsen, et al. (2025) `_ in **eLife** for more information

Key Metrics
-----------

- Transcripts per on-tissue square micrometer

  - Measure of transcript density, easily comparable between experiments

- Data loss

  - Individual field-of-view tiles with missing transcripts for ~10-100 genes

- Periodicity

  - Nonuniform transcript detection efficiency in x-, y-axes within FOV tiles

- 9/0 Ratio

  - Nonuniform transcript detection efficiency in z-axis throughout entire tissue

- Perfusion flow rate

  - Deviations from ideal fluidics can subtly impact transcript detection for a subset of genes

- Tissue integrity

  - Assessment of missing tissue from damage or gel detachment.


Contact
-------
paul.olsen@alleninstitute.org and naomi.martin@alleninstitute.org

Owner

  • Name: Allen Institute
  • Login: AllenInstitute
  • Kind: organization
  • Location: Seattle, WA

Please visit http://alleninstitute.github.io/ for more information.

GitHub Events

Total
  • Issues event: 4
  • Watch event: 5
  • Issue comment event: 3
  • Push event: 16
  • Fork event: 1
  • Create event: 1
Last Year
  • Issues event: 4
  • Watch event: 5
  • Issue comment event: 3
  • Push event: 16
  • Fork event: 1
  • Create event: 1

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 236
  • Total Committers: 3
  • Avg Commits per committer: 78.667
  • Development Distribution Score (DDS): 0.636
Past Year
  • Commits: 236
  • Committers: 3
  • Avg Commits per committer: 78.667
  • Development Distribution Score (DDS): 0.636
Top Committers
Name Email Commits
naomixmartin n****n@g****m 86
polsen99 1****9 84
Naomi Martin n****n@a****g 66
Committer Domains (Top 20 + Academic)
alleninstitute.org: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 4
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 2
  • Total pull request authors: 0
  • Average comments per issue: 0.25
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 4
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 0.25
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • KunHHE (3)
  • chenxiZ7 (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Dependencies

merquaco.egg-info/requires.txt pypi
  • imagecodecs *
  • matplotlib *
  • numpy *
  • opencv-python *
  • pandas *
  • scikit-image *
  • tifffile *
requirements.txt pypi
  • imagecodecs ==2024.1.1
  • matplotlib ==3.9.0
  • numpy ==1.26.4
  • opencv-python ==4.9.0.80
  • pandas ==2.2.2
  • scikit-image ==0.23.2
  • sphinx-rtd-theme ==2.0.0
  • tifffile ==2024.5.10
setup.py pypi