rt-utils
medicaldetectiontoolkit
rt-utils | medicaldetectiontoolkit | |
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2 | 2 | |
175 | 1,269 | |
2.9% | 0.3% | |
3.1 | 0.0 | |
10 days ago | 29 days ago | |
Python | Python | |
MIT License | Apache License 2.0 |
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rt-utils
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Trying to make masks from CT contours and need help...
I am trying to make masks from CT contours and need some help. I am using the rt_utils extension: https://github.com/qurit/rt-utils. I am having issues with the dicom_series_path - I set my path to be the folder all of the dicom slices are housed in, but I get "permission denied" as the function is looking for a file, not a folder. I then set the path to go directly to the first CT slice, and the function runs but creates an error due to there being no contour on that slice (understandable).
- Varian structure file to training masks
medicaldetectiontoolkit
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3D rcnn
Checkout https://github.com/MIC-DKFZ/medicaldetectiontoolkit, they have a recent 3d rcnn implementation. Their paper is a good start on the topic. Also have a look at nnDetection from the same group, it might provide some more leads. Hth
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3D Faster R-CNN for microscopy image analysis
I'm doing research in the area of biomedical image processing using deep learning. At the moment, I'm focused in the detection of biological structures in 3D microscopy images. For this task I trained a Faster R-CNN architecture, however I noticed that while the training loss is decreasing the validation loss is high, doesn't decrease and sometimes oscillates. When I looked at the results, the bounding boxes in the training and validation sets were too small but located at random spots. At first I thought that I should adjust the size of the anchors, however, even after trying different anchor sizes the results didn't improve. I would like to know if anyone has experience in working with 3D Faster R-CNN that could help me with suggestions for this project. (btw, I'm using the code available in this repo). Thanks in advance.
What are some alternatives?
pydicom - Read, modify and write DICOM files with python code
nnUNet
Phantom - Effective DICOM anonymization in Python
mmdetection3d - OpenMMLab's next-generation platform for general 3D object detection.
raiven - A framework for the translation of AI tools to the radiology environment
Mask-RCNN-TF2 - Mask R-CNN for object detection and instance segmentation on Keras and TensorFlow 2.0
mammography_metarepository - Meta-repository of screening mammography classifiers
BlenderProc - A procedural Blender pipeline for photorealistic training image generation
platipy - Processing Library and Analysis Toolkit for Medical Imaging in Python
MONAILabel - MONAI Label is an intelligent open source image labeling and learning tool.
PaddleDetection - Object Detection toolkit based on PaddlePaddle. It supports object detection, instance segmentation, multiple object tracking and real-time multi-person keypoint detection.
BCNet - Deep Occlusion-Aware Instance Segmentation with Overlapping BiLayers [CVPR 2021]