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JuliaHealth / MedImages.jl

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Supporting references and further reads for better understanding of the NIfTI and DICOM functionality. #3

Open divital-coder opened 6 months ago

divital-coder commented 6 months ago

Gist of dicom data in python https://towardsdatascience.com/dealing-with-dicom-using-imageio-python-package-117f1212ab82

Gist of NIfTI data in julia and python https://brainder.org/2012/09/23/the-nifti-file-format/ https://peerherholz.github.io/workshop_weizmann/data/image_manipulation_nibabel.html#

^ above are some good starting points for newbies, who might want to consider reading more about the ecosystem and capabilities. Feel free to include them in references as the documentation for the project grows!

divital-coder commented 5 months ago

The ITK implementation of loading nifti files, (consists up of stuff for loading and saving header and pixeldata from .nii) --ITK c++ nifti file loading --dicom to nifti python program which using numpy , pydicom and nibabel --guide on working nifti files

divital-coder commented 5 months ago

Sample Reference Medical Imaging dataset links : https://drive.google.com/drive/folders/1HqEgzS8BV2c7xYNrZdEAnrHk7osJJ--2 https://wiki.cancerimagingarchive.net/display/Public/RIDER+Lung+PET-CT https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=23691656

More comprehensive ones 👍🏻 https://github.com/icometrix/dicom2nifti/tree/main/tests/data https://nifti.nimh.nih.gov/nifti-1/data

divital-coder commented 5 months ago

For Generative Adversarial Networks (GAN's) resources for medical imaging check out "Awesome GAN for medical imaging on github"

divital-coder commented 5 months ago

Currently making a reference "memo or mem" for loading nifti file data, u can find that here : https://mem.ai/p/rWZ9et3sk1U5gkybJdNK

divital-coder commented 5 months ago

Important Reference from: nifti1._io.c file upon which ITKNiftiImageIO.cxx is based nifti1_io.h file upon which ITKNiftiImageIO.cxx is based

divital-coder commented 4 months ago

References (from SITK) for loading spatial metadata https://simpleitk.org/SimpleITK-Notebooks/01_Image_Basics.html https://simpleitk.org/SPIE2019_COURSE/02_images_and_resampling.html https://examples.itk.org/src/filtering/imagegrid/changeimageoriginspacingordirection/documentation https://simpleitk.readthedocs.io/en/master/fundamentalConcepts.html

divital-coder commented 1 month ago

Amazing data science in julia chapter based book under geospatial stuff, also include pixel array transforms information around orientation and spacing. https://juliaearth.github.io/geospatial-data-science-with-julia/05-transforms.html