The dataset is divided into two sub-folders - 'source' and 'target'. The 'source' folder has a total of 4,080 images of Chest X-rays. The 'target' folder has a total of 4,080 Dual-Energy subtracted images corresponding to the images present in 'source' folder.

Instructions: 

Detailed documentation is provided in the following link: https://github.com/hmchuong/ML-BoneSuppression

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This data set contains:

 

-88 patients

 

-the noncontrast computed tomography (NCCT) and computed tomography angiography (CTA) performed before thrombectomy.

 

-the VOI of blood clot for NCCT and CTA.

 

For each patient NCCT data is marked "2" and CTA is marked "1".

Instructions: 

For each patient NCCT data is marked "2" and CTA is marked "1".

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The concept of tuberculosis detection paves a major role in this recent world because, according to the Global Tuberculosis (TB) Report in 2019, more than one million cases are reported per year in India. Even though various tests are available, the chest X-ray is the most important one, without which the detection will be incomplete. In ancient poster anterior chest radiographs, several clinical and diagnostic functions are built by the use of computationally designed algorithms.

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The Magnetic Resonance – Computed Tomography (MR-CT) Jordan University Hospital (JUH) dataset has been collected after receiving Institutional Review Board (IRB) approval of the hospital and consent forms have been obtained from all patients. All procedures followed are consistent with the ethics of handling patients’ data.

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The Magnetic Resonance – Computed Tomography (MR-CT) Jordan University Hospital (JUH) dataset has been collected after receiving Institutional Review Board (IRB) approval of the hospital and consent forms have been obtained from all patients. All procedures followed are consistent with the ethics of handling patients’ data.

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 Histopathological characterization of colorectal polyps allows to tailor patients' management and follow up with the ultimate aim of avoiding or promptly detecting an invasive carcinoma. Colorectal polyps characterization relies on the histological analysis of tissue samples to determine the polyps malignancy and dysplasia grade. Deep neural networks achieve outstanding accuracy in medical patterns recognition, however they require large sets of annotated training images.

Instructions: 

In order to load the data, we provide below an example routine working within PyTorch frameworks. We provide two different resolutions, 800 and 7000 um/px.

Within each resolution, we provide .csv files, containing all metadata information for all the included files, comprising:

  • image_id;
  • label (6 classes - HP, NORM, TA.HG, TA.LG, TVA.HG, TVA.LG);
  • type (4 classes - HP, NORM, HG, LG);
  • reference WSI;
  • reference region of interest in WSI (roi);
  • resolution (micron per pixels, mpp);
  • coordinates for the patch (x, y, w, h).

Below you can find the dataloader class of UNITOPatho for PyTorch. More examples can be found here.


import torch

import torchvision

import numpy as np

import cv2

import os

 

class UNITOPatho(torch.utils.data.Dataset):

def __init__(self, df, T, path, target, subsample=-1, gray=False, mock=False):

self.path = path

self.df = df

self.T = T

self.target = target

self.subsample = subsample

self.mock = mock

self.gray = gray

allowed_target = ['type', 'grade', 'top_label']

if target not in allowed_target:

print(f'Target must be in {allowed_target}, got {target}')

exit(1)

print(f'Loaded {len(self.df)} images')
 

def __len__(self):

return len(self.df)

def __getitem__(self, index):

entry = self.df.iloc[index]

image_id = entry.image_id

image_id = os.path.join(self.path, entry.top_label_name, image_id)

img = None

if self.mock:

C = 1 if self.gray else 3

img = np.random.randint(0, 255, (224, 224, C)).astype(np.uint8)

else:

img = cv2.imread(image_id)

if self.subsample != -1:

w = img.shape[0]

while w//2 > self.subsample:

img = cv2.resize(img, (w//2, w//2))

w = w//2

img = cv2.resize(img, (self.subsample, self.subsample))

if self.gray:

img = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)

img = np.expand_dims(img, axis=2)

else:

img = cv2.cvtColor(img, cv2.COLOR_BGR2RGB)

if self.T is not None:

img = self.T(img)

return img, entry[self.target]

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This is a supplementary data file, providing the data used to evaluate the performance of our 3D fully convolutional neural network. This network removes reverberation noise from ultrasound channel data. This dataset is simulated ultrasound channel data, simulated in Field II Pro, and has artificial reverberation and thermal noise added. This dataset will be linked to our publication, once it is accepted. 

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