3d_u-vec

3D deep learning model to predict nucleus-Golgi vectors in 3D microscopy images of mouse retinas

3dimagenormalization

3dunet

testing code for docker

3dvascnet

Official implementation of the paper: Narotamo, H., Silveira, M., & Franco, C. A. (2024). 3DVascNet: An Automated Software for Segmentation and Quantification of Mouse Vascular Networks in 3D. Arteriosclerosis, Thrombosis, and Vascular Biology.

3dvox2vox

Official implementation of the paper accepted for presentation at EMBC 2022: "Synthetic Generation of 3D Microscopy Images using Generative Adversarial Networks"

3dyolo

3D Implementation of the Tiny Yolo v2 model to jointly detect nucleus-Golgi pairs in 3D Microscopy Images

butterfly_cnn

CNN’s for detection and measurement of butterfly eyespot patterns

cell-nucleus-and-membrane-segmentation-and-feature-extraction

clearmap2

ClearMap 2.0 with WobblyStitcher, TubeMap and CellMap

conv_index_iris_filter

Implementation of the iris filter to obtain the gradient convergence maps of nuclei in microscopy images. Developed for the paper: "Narotamo, H., Sanches, J. M., & Silveira, M. (2020, July). Combining deep learning with handcrafted features for cell nuclei segmentation."

dl_ecg_classification

Official implementation of the paper: "Deep learning for ECG classification: A comparative study of 1D and 2D representations and multimodal fusion approaches"

ec_analysis

Code for the study "Eph-ephrin signaling couples endothelial cell sorting and arterial specification" by Stewen J, Kruse K, Godoi-Filip AT, Jeong H, Adams S, Berkenfeld F, Stehling M, Red-Horse K, Adams RH, Pitulescu ME

hemaxin

interphasecellcyclestaging

Official implementation of the paper: "Narotamo, H., Fernandes, M. S., Moreira, A. M., Melo, S., Seruca, R., Silveira, M., & Sanches, J. M. (2021). A machine learning approach for single cell interphase cell cycle staging. Scientific reports."

mask_rcnn

Mask R-CNN for object detection and instance segmentation on Keras and TensorFlow

polarity-vectors

A Deep-Learning Approach for Vectors Prediction in 3D Microscopy Images

scitsr

Table structure recognition dataset of the paper: Complicated Table Structure Recognition

stardist

StarDist - Object Detection with Star-convex Shapes

vesselvio

VesselVio is an open-source application for the analysis and visualization of segmented vasculature datasets

xml-files-based-on-pascal-voc-format-from-binary-segmentation-masks

yolo_unet

Official implementation of the paper: "Narotamo, H., Sanches, J. M., & Silveira, M. (2019, July). Segmentation of Cell Nuclei in Fluorescence Microscopy Images Using Deep Learning. "