Data

Tools

Indexes

Applications

Experiments

Open Source Science

swelling_tablet_fronts_d_k_from_mri_t2_or_img

Tool for calculating swelling tablet eroding front's diffusion rate D and the rate of the swelling k from time series of either T2-maps or MRI images in FDF or Text Image format. (Python 3)

https://github.com/beatawereszczynska/swelling_tablet_fronts_d_k_from_mri_t2_or_img

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 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.9%) to scientific vocabulary

Keywords

agilent data-analysis data-visualization diffusion diffusion-coefficient exe image image-analysis image-processing jupyter-notebook machine-learning mri mri-analysis mri-applications mri-data mri-image mri-images python python3 t2-mapping
Last synced: 6 months ago · JSON representation

Repository

Tool for calculating swelling tablet eroding front's diffusion rate D and the rate of the swelling k from time series of either T2-maps or MRI images in FDF or Text Image format. (Python 3)

Basic Info
  • Host: GitHub
  • Owner: BeataWereszczynska
  • License: other
  • Language: Jupyter Notebook
  • Default Branch: main
  • Homepage:
  • Size: 70.4 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Topics
agilent data-analysis data-visualization diffusion diffusion-coefficient exe image image-analysis image-processing jupyter-notebook machine-learning mri mri-analysis mri-applications mri-data mri-image mri-images python python3 t2-mapping
Created over 3 years ago · Last pushed almost 3 years ago
Metadata Files
Readme License Citation

README.md

SwellingtabletfrontsDkfromMRIT2or_img

DOI

Tool for characterizing the swelling of tablets immersed in a solution. Creates time plots and calculates eroding front's diffusion rate D and the rate of the swelling k from time series of either T2-maps or (properly contrasted, e.g. T2-weighted) MRI images in FDF (file format native for Agilent MRI scanners) or Text Image format. This software is suitable for swelling matrix tablets forming a membrane-like structure in contact with the solution in which they are immersed.

Graphical abstract

The repository contains:

  1. Python script Dkfrom_T2maps.py - the main version of the software.
  2. Jupyter notebook file notebookDkfromT2maps.ipynb presenting:
  3. short introduction to the topic in which the software can be usefull,
  4. input parameters and their meanings,
  5. how the code works step by step,
  6. sample results with commentary.
  7. PDF version of the Jupyter notebook file notebookDkfromT2maps.pdf.
  8. EXE file for non-coders DkfromT2mapsvB_win10.exe (compiled for Windows 10) that can be used simply by double-clicking, taking input parameters from an input file. This program only accepts Text Images as an input (I had troubles compyling a script utilizing itk - python library enabling FDF import). HINT: Most of image files can be converted to Text Image format using ImageJ (https://imagej.nih.gov/ij/download.html). To import FDF files by ImageJ you'll need Multi FDF Opener plugin (https://imagej.nih.gov/ij/plugins/multi-opener.html).
  9. Python script used for creating the EXE file: DkfromT2mapsvB.py.
  10. Sample input file for DkfromT2mapsvB: INPUT-DkfromT2mapsvB.txt.
  11. Sample MRI-derived T2-maps in FDF format in MRI_FDF folder.
  12. Sample MRI-derived T2-maps in Text Image format in MRI_TXTimages folder.
  13. Sample results in D_results folder.
  14. Graphical abstract GraphAbstr.jpg.

License

The software is licensed under the MIT license. The non-software content of this project is licensed under the Creative Commons Attribution 4.0 International license. See the LICENSE file for license rights and limitations.

You may also like

MRIk-space-deriveddetails_edges - k-space based details/edges detection in MRI images with optional k-space based denoising and detail control (data import suitable for Agilent FID files, three binarization methods to choose from), https://doi.org/10.5281/zenodo.7388435 (https://github.com/BeataWereszczynska/MRIk-space-deriveddetails_edges).

squareimgfragments - saving random unique square fragments of an image (located inside or outside defined bounding box) as jpg (https://github.com/BeataWereszczynska/squareimgfragments).

Owner

  • Name: Beata Wereszczyńska
  • Login: BeataWereszczynska
  • Kind: user
  • Location: Poland

I'm a Python enthusiast, but also an NMR and MRI physicist (PhD) with broad experience in experimental research.

GitHub Events

Total
Last Year

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 49
  • Total Committers: 1
  • Avg Commits per committer: 49.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 49
  • Committers: 1
  • Avg Commits per committer: 49.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Beata Wereszczyńska b****a@g****m 49

Issues and Pull Requests

Last synced: about 2 years ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total 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
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
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels