Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/brainglobe/brainglobe-ccf-translator

A tool for translating between common coordinate frameworks using deformation matrices.

https://github.com/brainglobe/brainglobe-ccf-translator

Science Score: 49.0%

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
    Found 1 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: biorxiv.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.2%) to scientific vocabulary
Last synced: 7 months ago · JSON representation

Repository

A tool for translating between common coordinate frameworks using deformation matrices.

Basic Info
  • Host: GitHub
  • Owner: brainglobe
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 13.2 MB
Statistics
  • Stars: 7
  • Watchers: 4
  • Forks: 0
  • Open Issues: 11
  • Releases: 0
Created almost 2 years ago · Last pushed 8 months ago
Metadata Files
Readme License Codemeta

README.md

brainglobe-ccf-translator

PyPI - Version

CCF translator (brainglobe-ccf-translator) is a tool for translating between common coordinate frameworks using deformation matrices. A longstanding problem in NeuroInformatics has been the inability to easily translate data between common coordinate frameworks. CCF translator aims to solve this. By connecting each new space to an existing one, we can construct a graph of deformations. This means that data can be translated as long as there is a route from one space to another, even if that route passes through multiple other spaces. Now, when new templates for new modalities, strains, or ages are released, users will not be subdivided into unrelated spaces. As long as they are connected to a space which exists in our network, they will be fully connected to all other spaces.

CCF translator can also interpolate between spaces and create a new intermediate space. This is primarily useful for development, where, for instance, the midpoint between day 5 and day 7 can be taken and used as a postnatal day 6 reference. It could also be useful for making references of disease progression.

a graph of all the available spaces and how they are connected. the spaces are nodes with the space name written on top of them, the edges show which spaces are connected to which other spaces.

Use Cases

One way you can use CCF translator is to view data from one space, in another space. For instance the allen connectivity dataset shows projections from viral tracing studies in the adult brain. We can take any of these projection datasets and view them in the developing brain, for instance post natal day 9. an image which shows a viral tracing study overlaid on the allen adult ccfv3 template. it shows that same viral tracing data transformed and overlaid on a post natal day 9 template. between the two images is an arrow pointing from the adult to the post natal day 9 brain, above which is text saying CCF translator, implying that CCF translator was used to transform the data from adult to post natal day 9.

Installation

CCF translator can be installed by running pip install brainglobe-ccf-translator

Currently supported spaces

the name in CCF translator aims to copy the name of atlases in the brainglobeatlasapi when possible. | Framework Name | name in api | supported age range | -------------- | ----------- | ----------- | Allen mouse CCFv3 | allenmouse | 56 | Demba developmental mouse | dembadevmouse| 4-56 | Gubra lightsheet mouse | perenslsfmmouse| 56 | Gubra MRI mouse | perensmrimouse| 56 | Gubra STPT mouse | perensstptmouse| 56 | Princeton lighsheet mouse | princeton_mouse| 56

Usage

Transforming points To take a coordinate in one volume and find the equivalent coordinate in a second volume is quite simple in CCF translator. ```python import numpy as np import brainglobeccftranslator

points = np.array([(286,250,267), (414,247,452)]) pset = brainglobeccftranslator.PointSet(points, 'dembadevmouse', voxelsizemicron=20, agePND=56) pset.transform(targetage=56, targetspace='allenmouse') print(f"new points are {pset.values}")

new points are [[267 250 286] [452 247 414]] ``` Transforming volumes

To run the volume examples you will want to install brainglobe-atlasapi using the following pip install brainglobe-atlasapi

Transforming a volume is equally simple, here we get the volume from the brainglobe api, but you can load it however you like. In the Demba space the valid ages are from 4 to 56, and all of these are valid targets for transformation. ```python from brainglobeatlasapi.bgatlas import BrainGlobeAtlas import brainglobeccftranslator

voxelsizemicron = 10 spacename = r"allenmouse" atlas = BrainGlobeAtlas("{spacename}{voxelsizemicron}um") sourceage = 56 targetage= 32

ccftvol = brainglobeccftranslator.Volume( values = atlas.reference, space = 'allenmouse', voxelsizemicron=voxelsizemicron, segmentationfile=False, agePND = source_age )

ccftvol.transform(targetage, 'dembadevmouse') ccftvol.save(rf"demodata/P{targetage}template{voxelsize_micron}um.nii.gz") ```

Contributing

If you would like to add a new space or connect an existing one, please create a deformation matrix and/or describe the required reorientation, flipping, cropping, and padding of the axis between this space and one that already exists in the network, and then open an issue in this repository. Ideally, choose a space which covers all the areas which are covered in your space. While the Allen CCFv3 is very popular, it is missing the anterior olfactory bulb and the caudal portion of the cerebellum and brain stem, so it is not the optimal choice.

Citation

CCF translator was first described in DeMBA: a developmental atlas for navigating the mouse brain in space and time. If you use CCF translator, please cite that paper.

Owner

  • Name: BrainGlobe
  • Login: brainglobe
  • Kind: organization
  • Location: London/Munich

Open python tools for morphological analyses in systems neuroscience

CodeMeta (codemeta.json) 

{
  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
  "type": "SoftwareSourceCode",
  "author": [
    {
      "id": "https://orcid.org/0000-0002-4111-6259",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "Division of Anatomy, University of Oslo"
      },
      "email": "harry.carey@medisin.uio.no",
      "familyName": "Carey",
      "givenName": "Harry"
    },
    {
      "type": "schema:Role",
      "schema:author": "https://orcid.org/0000-0002-4111-6259"
    },
    {
      "id": "https://orcid.org/0000-0002-2926-6836",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "Pennsylvania State University"
      },
      "email": "i.e.bjerke@medisin.uio.no",
      "familyName": "Bjerke",
      "givenName": "Ingvild "
    },
    {
      "id": "https://orcid.org/0000-0002-4458-6870",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "Sainsbury Wellcome Centre"
      },
      "email": "adam@adamltyson.com",
      "familyName": "Tyson",
      "givenName": "Adam"
    }
  ],
  "codeRepository": "https://github.com/brainglobe/brainglobe-ccf-translator",
  "dateCreated": "2024-05-24",
  "dateModified": "2024-11-18",
  "description": "CCF translator (brainglobe-ccf-translator) is a tool for translating between common coordinate frameworks using deformation matrices. A longstanding problem in NeuroInformatics has been the inability to easily translate data between common coordinate frameworks. CCF translator aims to solve this. By connecting each new space to an existing one, we can construct a graph of deformations. This means that data can be translated as long as there is a route from one space to another, even if that route passes through multiple other spaces. Now, when new templates for new modalities, strains, or ages are released, users will not be subdivided into unrelated spaces. As long as they are connected to a space which exists in our network, they will be fully connected to all other spaces.\n\nCCF translator can also interpolate between spaces and create a new intermediate space. This is primarily useful for development, where, for instance, the midpoint between day 5 and day 7 can be taken and used as a postnatal day 6 reference. It could also be useful for making references of disease progression.",
  "downloadUrl": "https://files.pythonhosted.org/packages/c2/24/677f016dbc9041e450329cc16c582cffd39ac4f79685de994596ea9da62f/brainglobe_ccf_translator-0.21.tar.gz",
  "funder": {
    "type": "Organization",
    "name": "European Union "
  },
  "keywords": [
    "Neuroscience",
    "Neuroinformatics",
    "atlasing",
    "CCF"
  ],
  "license": "https://spdx.org/licenses/MIT",
  "name": "brainglobe-ccf-translator",
  "programmingLanguage": "Python 3",
  "relatedLink": "https://pypi.org/project/brainglobe-ccf-translator/",
  "version": "0.21.0",
  "developmentStatus": "wip",
  "funding": "European Unions Horizon 2020 Framework Program for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3) ",
  "issueTracker": "https://github.com/brainglobe/brainglobe-ccf-translator/issues",
  "referencePublication": "https://doi.org/10.1101/2024.06.14.598876"
}

GitHub Events

Total
  • Issues event: 1
  • Watch event: 1
  • Issue comment event: 8
  • Push event: 9
  • Pull request review event: 3
  • Pull request review comment event: 2
  • Pull request event: 4
  • Create event: 2
Last Year
  • Issues event: 1
  • Watch event: 1
  • Issue comment event: 8
  • Push event: 9
  • Pull request review event: 3
  • Pull request review comment event: 2
  • Pull request event: 4
  • Create event: 2

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 100
  • Total Committers: 3
  • Avg Commits per committer: 33.333
  • Development Distribution Score (DDS): 0.05
Past Year
  • Commits: 40
  • Committers: 1
  • Avg Commits per committer: 40.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
polarbean h****5@g****m 95
Harry Carey 3****n@u****m 4
polarbean h****c@U****9 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 3
  • Total pull requests: 5
  • Average time to close issues: N/A
  • Average time to close pull requests: 2 days
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.4
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 5
  • Average time to close issues: N/A
  • Average time to close pull requests: 2 days
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.4
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • PolarBean (2)
  • adamltyson (1)
Pull Request Authors
  • PolarBean (5)
Top Labels
Issue Labels
enhancement (3)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 18 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
pypi.org: brainglobe-ccf-translator

a package to translate data between common coordinate frameworks

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 18 Last month
Rankings
Dependent packages count: 10.0%
Average: 33.2%
Dependent repos count: 56.4%
Maintainers (1)
polarbean
Last synced: 7 months ago