QTIM Lab (@QTIM-Lab)
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Top repositories

1

DeepNeuro

A deep learning python package for neuroimaging data. Made by:
Jupyter Notebook
122
star
2

qtim_Tutorials

Jupyter notebooks and other tutorials for medical imaging and deep learning, courtesy of the QTIM lab.
Jupyter Notebook
28
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3

SiameseChange

Python
17
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4

qtim_ROP

Code base for preprocessing, segmentation and classification of retinal images
Python
14
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5

qtim_tools

A set of tools used for quantitative analysis of and machine learning from 3D medical images. Created by the Quantitative Tumor Imaging Lab at Martinos.
HTML
11
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6

Assessing-Saliency-Maps

Python
10
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7

DeepRad

A deep learning python package for medical imaging data.
Python
6
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8

qtim_PreProcessor

Resources and pipelines used for pre-processing medical imaging data at the Quantitative Tumor Imaging Lab at the Martinos Center (MIT/HST). Includes Docker resources.
Python
6
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9

SlicerSegmentationWizard

This is a 3D model-based segmentation tool for 3D Slicer. It includes utilities for calculating subtraction maps and thresholding intensities. It can be downloaded as an extension to 3D Slicer.
Python
4
star
10

PXS-score

TBD
Python
4
star
11

brats2017

Submission for BRATS 2017
Python
4
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12

qtim-lab.github.io

A repository for the public-facing web page of the Quantiative Tumor Imaging Lab at the Martinos Center.
HTML
4
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13

dinov2_imagenet1k_example

To get DinoV2 running on a non-slurm environment on ImageNet 1K
Python
4
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14

FeaturePrediction_ROP

Networks to predict systemic features such as gender and age in ROP
Python
3
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15

dl-prediction-brca-tiph

Implementation of the paper "Deep Learning-based Prediction of Breast Cancer Tumor and Immune Phenotypes from Histopathology" by Tiago Gonçalves, Dagoberto Pulido-Arias, Julian Willett, Katharina V. Hoebel, Mason Cleveland, Syed Rakin Ahmed, Elizabeth Gerstner, Jayashree Kalpathy-Cramer, Jaime S. Cardoso, Christopher P. Bridge and Albert E. Kim.
Python
3
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16

trame_optimeyes

trame tools and visualizations
Python
2
star
17

MedICI

Composite Challenge Platform
Python
2
star
18

AdrenalMGB-Version-1

Preprocessing and neural network code to train an adrenal gland segmenter and classifier using contrast CT abdominal imaging.
Python
2
star
19

3D_CNN_Regression

A model for using input 3D volumes for creating scalar output 3D volumes
Python
2
star
20

qtim_gbmSegmenter

This is a self-contained Docker container for segmenting high- and low-grade glioblastomas in MR scans using deep learning.
Python
1
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21

qtim_vessels

1
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22

CU_Project_Template

A template for using the CU environments and tracking generated data
Python
1
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23

deeprop

A web-based telemedicine platform for retinopathy of prematurity
Python
1
star
24

monaiLabelExploration

Get MonaiLabel server running and establish an input output workflow
Python
1
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25

DeepTofts

Python
1
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26

Addressing-catastrophic-forgetting-for-medical-domain-expansion

1
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27

qtim_DCE

A collection of open-source DCE analysis programs in Python, Matlab, and 3D Slicer.
MATLAB
1
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28

Image-Comparator

Updated Image Comparator and Classifier
Jupyter Notebook
1
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29

RetinavsFace_ROP

Python
1
star
30

neurofit

A python library for fitting neuroscience algorithms with deep learning methods.
1
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31

ROP_app

Java
1
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32

MedSAM

Intro to MedSAM Model
Jupyter Notebook
1
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33

LLM-Report-Labeling

Jupyter Notebook
1
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34

FL_ViT_pretraining

Python
1
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35

preprocessing

`preprocessing` is a python library designed for the purpose of preprocessing MRI data at QTIM. It currently supports reorganization of dicom and nifti files to follow BIDS conventions, dicom to nifti conversion, and preprocessing for brain data. Its outputs are intended to follow the BIDS organizational scheme.
Python
1
star
36

federatedLearning_glaucoma_segmentation

Federated Learning Optic Disc and Cup Segmentation Model for Glaucoma Monitoring in Color Fundus Photographs(CFPs)
Python
1
star