Software developed by Biomedical Engineering group and referenced in papers
1. Three-stage classification of Alzheimer’s disease in MRI
Paper: “Three-stage classification of Alzheimer’s disease in MRI in clinical records of the Mass General Brigham Health Care System.”
2. Deep Learning Systems For Lymphoma Diagnostics
Paper: “Design and clinical validation of a point-of-care device for the diagnosis of lymphoma via contrast-enhanced microholography and machine learning.”
This code is part of a project to leverage deep learning systems for lymphoma diagnostics. We use the Maximally Stable Extrema Regions (MSER) blob detection algorithm to find regions of interest in a hologram image of cells and use a trained Convolutional Neural Network (CNN) to filter out non-cell regions.
– Detects cells in a hologram using the MSER algorithm and a pre-trained CNN.
- Contains several helper functions for processing multiple images from a single folder, or multiple folders that each contain multiple images.
- Contains the code to construct a CNN using Keras.
- Can load a pre-trained CNN or build an empty architecture and train it.
- Contains helper function to properly format and classify an input region with a pre-trained CNN.
- Contains numerous functions to load labelled training images from a directory into (x,y) training tensors.
- Can pre-process data to make for easier training.
- Designed to return data in a format that the region filter CNN can be trained with.
3. Cell Segmentation for Breast Cancer Cells
Paper: "CytoPAN – Portable cellular analyses for rapid point-of-care cancer diagnosis.”
This Matlab code is part of a project to identify breast cancer cells in bright-field and measure the mean fluorescence intensity of respective cells in fluorescence imaging for breast cancer biomarkers (QUAD, HER2, ERPR).
- Sobel edge detection method was used to determine cellular edges based on high contrast in the bright-field image.
- Binary gradient mask underwent dilation, hole filling, and smoothing
- Mask regions correlated with DAPI signals are identified as biological cells.
- Mean intensities of biomarkers (QUAD, HER2 and ERPR) of individual biological cells are measured.
4. R-Script and Data Files for EV Protein Search
Paper: "A high-throughput magneto-electrochemical array for the integrated isolation and profiling of extracellular vesicles from plasma”
The following files are used to search EV protein markers for colorectal cancer diagnosis.
– R script to load and filter datasets from public databases, and to compare protein expression levels between normal and tumor tissues.
– HTML output generated by Marker_selection.Rmd.
– List of EV proteins retrieved from EVpedia.