The database is organized in 2 folders and documentation:
• Data – raw signal recordings for the individual participants, including extracted Inter-Beat-Interval sequence and participants’ respond in N-back task
• Subjective_rating – subjective rating of sleep quality and NASA-TLX
• MAUS_Documentation.pdf – documentation of dataset description and details.

This datasest contains a zip folder of 80 mammograms and an excel file having mammographic features, histopathological features as well as clinical fatures of all the patients. 

IMPORTANT:

If you use this dataset, please cite below publications-

1. Anubha Gupta, Rahul Duggal, Shiv Gehlot, Ritu Gupta, Anvit Mangal, Lalit Kumar, Nisarg Thakkar, and Devprakash Satpathy, "GCTI-SN: Geometry-Inspired Chemical and Tissue Invariant Stain Normalization of Microscopic Medical Images," Medical Image Analysis, vol. 65, Oct 2020. DOI: https://doi.org/10.1016/j.media.2020.101788. (2020 IF: 11.148)
2. Shiv Gehlot, Anubha Gupta and Ritu Gupta, "EDNFC-Net: Convolutional Neural Network with Nested Feature Concatenation for Nuclei-Instance Segmentation," ICASSP 2020 - 2020 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Barcelona, Spain, 2020, pp. 1389-1393.
3. Anubha Gupta, Pramit Mallick, Ojaswa Sharma, Ritu Gupta, and Rahul Duggal, "PCSeg: Color model driven probabilistic multiphase level set based tool for plasma cell segmentation in multiple myeloma," PLoS ONE 13(12): e0207908, Dec 2018. DOI: 10.1371/journal.pone.0207908

We have provided the copy of forms used to collect data for datset and a read me guide to undertand the features provided in dataset along with the content of all the 6 dataset submitted in excel sheet format.

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

The data contained in the first sheet of the dataset is in tidy format (each row correspond to an observation) and can be directly imported in R and elaborated with the package Tidyverse. It should be noticed that the row with the standard order 49 correspond to the reference degumming while the row 50 correspond to the test made on the bare silk fiber (not degummed). In this last case neither the mass loss nor the secondary structures were determined. In fact, being not degummed the sericine was surrounding the fiber so the examination of the secondary structure could not be done. The first two column of the dataset represent the Standard order (the standard order in which the Design of Experiment data are elaborated) and the Run order (the randomized order in whcih the trials were performed). The next four columns are the Studied factors while the rest of the dataset reports the process yields (in this case, the properties of the outcoming silk fibers). 

The second sheet contains the information of the molecular weight of the tested samples. In this case only one sample for each triplicate was tested. Both the standard order and the run order referred to the same samples of the first sheet. 

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]