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ENABLING 3D SEGMENTATION FOR DETECTING KIDNEY TUMORS

Radiologists use CT (Computed Tomography) and MRI (Magnetic Resonance Imaging) to diagnose and stage cancers. With recent advances in machine learning research in oncology, these images are used to train and automatically detect cancerous tissues. These scans are obtained at a pixel spacing of 0.5mm-1.5mm, which can result in volumes that range from 128x128x128 to 512x512x512.

ENABLING 3D SEGMENTATION FOR DETECTING KIDNEY TUMORS

One of the common tasks on these datasets is to segment regions of interest such as tumors/cysts on specific organs. If these masses are small enough, then using a lower resolution image can lead a model to ignore those sections. A large number of researchers work on models that can accurately segment out tumors in these medical scans. The biggest constraint for these kinds of models and high resolution datasets is memory resources.

segmentation

Most architectures that support machine learning applications run out of memory due to the large size of intermediate activation maps in the network. Using data or model parallelism does not solve this problem. Therefore, the most common alternative used in these cases is downsampling the volumes to a lower voxel space or training models on smaller crops of the volume. This can lead to a loss of contextual cues and therefore suboptimal performance on the dataset.

We hypothesize that training models on the true resolution of the dataset will help achieve better accuracy.

Do more pixels lead to better accuracy?
Do more pixels lead to better accuracy?

In our experiments, we use the open source dataset for kidney tumor segmentation.

QUANTITATIVE ANALYSIS
We train different models with different patch sizes in order to test the claim “More pixels leads to better accuracy”. We use Dice Score as a predictor of our performance. Dice scores essentially capture the similarity between two samples using Intersection Over Union:
QUANTITATIVE ANALYSIS
QUANTITATIVE ANALYSIS
QUALITATIVE ANALYSIS
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case1Header.d793d798 rgbImage.716953cd

To demonstrate the effect of increasing patch sizes on the accuracy of the model, here are a few visualizations:

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True Segmentation
Ground Truth
True Segmentation
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section2SmallImage3
Segmentation
64 Segmentation
section3SmallImage1
section3SmallImage2
section3SmallImage3
True Segmentation
128 Segmentation
case 2 case2HeaderMobile.0b548981
section1SmallImage1-1
section1SmallImage2-1
section1SmallImage3-1
section1SmallImage4-1
Ground Truth
section2SmallImage1-1
section2SmallImage2-1
section2SmallImage3-1
section2SmallImage4-1
64 Segmentation
True Segmentation
True Segmentation
True Segmentation
True Segmentation
128 Segmentation
conclusion.c82db71a conclusionMobile.dc64839b

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