beatawereszczynska/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)

Swelling_tablet_fronts_D_k_from_MRI_T2_or_img

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.

The repository contains:

1. Python script D_k_from_T2maps.py - the main version of the software.
2. Jupyter notebook file notebook_D_k_from_T2maps.ipynb presenting:

• short introduction to the topic in which the software can be usefull,
• input parameters and their meanings,
• how the code works step by step,
• sample results with commentary.

3. PDF version of the Jupyter notebook file notebook_D_k_from_T2maps.pdf.
4. EXE file for non-coders D_k_from_T2maps_vB_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).
5. Python script used for creating the EXE file: D_k_from_T2maps_vB.py.
6. Sample input file for D_k_from_T2maps_vB: INPUT-D_k_from_T2maps_vB.txt.
7. Sample MRI-derived T₂-maps in FDF format in MRI_FDF folder.
8. Sample MRI-derived T₂-maps in Text Image format in MRI_TXTimages folder.
9. Sample results in D_results folder.
10. 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.

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