Instance Segmentation of Unlabeled Modalities via Cyclic Segmentation GAN

no code implementations • 6 Apr 2022 • Leander Lauenburg, Zudi Lin, Ruihan Zhang, Márcia dos Santos, Siyu Huang, Ignacio Arganda-Carreras, Edward S. Boyden, Hanspeter Pfister, Donglai Wei

Instance segmentation for unlabeled imaging modalities is a challenging but essential task as collecting expert annotation can be expensive and time-consuming.

Generative Adversarial Network Image Segmentation +4

Deep learning based domain adaptation for mitochondria segmentation on EM volumes

1 code implementation • 22 Feb 2022 • Daniel Franco-Barranco, Julio Pastor-Tronch, Aitor Gonzalez-Marfil, Arrate Muñoz-Barrutia, Ignacio Arganda-Carreras

This is a problem known as domain adaptation, since models that learned from a sample distribution (or source domain) struggle to maintain their performance on samples extracted from a different distribution or target domain.

Self-Supervised Learning Style Transfer +1

NucMM Dataset: 3D Neuronal Nuclei Instance Segmentation at Sub-Cubic Millimeter Scale

1 code implementation • 13 Jul 2021 • Zudi Lin, Donglai Wei, Mariela D. Petkova, Yuelong Wu, Zergham Ahmed, Krishna Swaroop K, Silin Zou, Nils Wendt, Jonathan Boulanger-Weill, Xueying Wang, Nagaraju Dhanyasi, Ignacio Arganda-Carreras, Florian Engert, Jeff Lichtman, Hanspeter Pfister

Segmenting 3D cell nuclei from microscopy image volumes is critical for biological and clinical analysis, enabling the study of cellular expression patterns and cell lineages.

Instance Segmentation Representation Learning +1

AxonEM Dataset: 3D Axon Instance Segmentation of Brain Cortical Regions

1 code implementation • 12 Jul 2021 • Donglai Wei, Kisuk Lee, Hanyu Li, Ran Lu, J. Alexander Bae, Zequan Liu, Lifu Zhang, Márcia dos Santos, Zudi Lin, Thomas Uram, Xueying Wang, Ignacio Arganda-Carreras, Brian Matejek, Narayanan Kasthuri, Jeff Lichtman, Hanspeter Pfister

Electron microscopy (EM) enables the reconstruction of neural circuits at the level of individual synapses, which has been transformative for scientific discoveries.

Instance Segmentation Segmentation +1

Stable deep neural network architectures for mitochondria segmentation on electron microscopy volumes

1 code implementation • 8 Apr 2021 • Daniel Franco-Barranco, Arrate Muñoz-Barrutia, Ignacio Arganda-Carreras

For that reason, and following a recent code of best practices for reporting experimental results, we present an extensive study of the state-of-the-art deep learning architectures for the segmentation of mitochondria on EM volumes, and evaluate the impact in performance of different variations of 2D and 3D U-Net-like models for this task.

Hippocampus Segmentation

Inferring spatial relations from textual descriptions of images

1 code implementation • 1 Feb 2021 • Aitzol Elu, Gorka Azkune, Oier Lopez de Lacalle, Ignacio Arganda-Carreras, Aitor Soroa, Eneko Agirre

Previous work did not use the caption text information, but a manually provided relation holding between the subject and the object.

Common Sense Reasoning Object +1

MitoEM Dataset: Large-scale 3D Mitochondria Instance Segmentation from EM Images

1 code implementation • Medical Image Computing and Computer Assisted Intervention 2020 • Donglai Wei, Zudi Lin, Daniel Franco-Barranco, Nils Wendt, Xingyu Liu, Wenjie Yin, Xin Huang, Aarush Gupta, Won-Dong Jang, Xueying Wang, Ignacio Arganda-Carreras, Jeff Lichtman, Hanspeter Pfister

On MitoEM, we find existing instance segmentation methods often fail to correctly segment mitochondria with complex shapes or close contacts with other instances.

3D Instance Segmentation Segmentation +1

Deep Learning on Chest X-ray Images to Detect and Evaluate Pneumonia Cases at the Era of COVID-19

no code implementations • 5 Apr 2020 • Karim Hammoudi, Halim Benhabiles, Mahmoud Melkemi, Fadi Dornaika, Ignacio Arganda-Carreras, Dominique Collard, Arnaud Scherpereel

Tailored deep learning models are proposed to detect pneumonia infection cases, notably viral cases.

3D Object Detection From LiDAR Data Using Distance Dependent Feature Extraction

1 code implementation • 2 Mar 2020 • Guus Engels, Nerea Aranjuelo, Ignacio Arganda-Carreras, Marcos Nieto, Oihana Otaegui

Top view images are generated from point clouds as input for the networks.

3D Object Detection object-detection +1

Consistent and elastic registration of histological sections using vector-spline regularization

1 code implementation • Computer Vision Approaches to Medical Image Analysis 2006 • Ignacio Arganda-Carreras, Carlos O. S. Sorzano, Roberto Marabini, José María Carazo, Carlos Ortiz-de-Solorzano, Jan Kybic

Here we present a new image registration algorithm for the alignment of histological sections that combines the ideas of B-spline based elastic registration and consistent image registration, to allow simultaneous registration of images in two directions (direct and inverse).

BIRL Image Registration