pydicom-seg
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razorx89
Python package for DICOM-SEG medical segmentation file reading and writing
Currently, only the 3D reading and writing is implemented (e.g. MRI, CT), similiar to the dmcqi project. In my opinion, this covers the most common use case for e.g. image...
I am using `pydicom-seg` to create some dicomseg overlays for chest XRay dicom. The segmentations are multiclass and overlapping in nature. Currently, I pass a 3D NumPy array to make...
Hi, I'm working on a series that has several instances/slices with varying orientations. When I paint a segmentation on several instances that do not share an orientation, only the first...
ITK now directly supports python wrapping. The wrapping provided directly by ITK is arguably more Pythonic, and it expose the entire ITK library and all optional modules, whereas SimpleITK does...
Hi! I am working on conversion of images to dicom using pydicom, which is successful. However, when I create a segmentation for it, it is getting saved but I'm seeing...
Hi, I would like to create an empty DICOM-SEG from a json file as created with http://qiicr.org/dcmqi/#/seg to then use it as a template for users to fill in the...
`SurfaceSegmentationStorage` is a special type of segmentation where the segments are represented by polygonal meshes instead of voxel-based annotation. https://dicom.innolitics.com/ciods/surface-segmentation A conversion script could read a `SurfaceSegmentationStorage` DICOM and write...
Dear @razorx89, I have recently started working on a new project which involves visualizing "[fractional segmentations](https://dicom.nema.org/medical/Dicom/2018d/output/chtml/part03/sect_C.8.20.2.3.html)", i.e. looking at a segmentation as a probability map, rather than fixed labels for...
Hello, thank you for sharing this project! Are there any plans to support writing of multi-label segmentations as well? I have some overlapping structures and, I would want to store...
This is what I'm trying: ``` # read individual segments from dicom file via pydicom_seg dcm = pydicom.dcmread(dicom_filename) print(dcm.pixel_array.shape) # Use a SegmentReader to iterate through all the segments reader...
