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Catherine Bouchard

PhD - Université Laval
Supervisor
Christian Gagné
Research Topics
Computer Vision
Deep Learning
Generative Models
Medical Machine Learning
Google Scholar
GitHub

Publications

Filtering Pixel Latent Variables for Unmixing Noisy and Undersampled Volumetric Images
Catherine Bouchard
Andréanne Deschênes
Vincent Boulanger
Jean-Michel Bellavance
Julia Chabbert
Alexy Pelletier-Rioux
Flavie Lavoie-Cardinal
Christian Gagné
2023-12-08
ArXiv (preprint)
arxiv.org
arxiv.org
Unmixing Optical Signals from Undersampled Volumetric Measurements by Filtering the Pixel Latent Variables
Catherine Bouchard
Andréanne Deschênes
Vincent Boulanger
Jean-Michel Bellavance
Julia Chabbert
Alexy Pelletier-Rioux
Flavie Lavoie-Cardinal
Christian Gagné
2023-12-08
ArXiv (preprint)
arxiv.org
arxiv.org
Unmixing Optical Signals from Undersampled Volumetric Measurements by Filtering the Pixel Latent Variables
Catherine Bouchard
Andréanne Deschênes
Vincent Boulanger
Jean-Michel Bellavance
Julia Chabbert
Alexy Pelletier-Rioux
Flavie Lavoie-Cardinal
Christian Gagné
The development of signal unmixing algorithms is essential for leveraging multimodal datasets acquired through a wide array of scientific im… (see more)aging technologies, including hyperspectral or time-resolved acquisitions. In experimental physics, enhancing the spatio-temporal resolution or expanding the number of detection channels often leads to diminished sampling rate and signal-to-noise ratio (SNR), significantly affecting the efficacy of signal unmixing algorithms. We propose Latent Unmixing, a new approach which applies band-pass filters to the latent space of a multi-dimensional convolutional neural network to disentangle overlapping signal components. It enables better isolation and quantification of individual signal contributions, especially in the context of undersampled distributions. Using multi-dimensional convolution kernels to process all dimensions simultaneously enhances the network's ability to extract information from adjacent pixels, and time- or spectral-bins. This approach enables more effective separation of components in cases where individual pixels do not provide clear, well-resolved information. We showcase the method's practical use in experimental physics through two test cases that highlight the versatility of our approach: fluorescence lifetime microscopy and mode decomposition in optical fibers. The latent unmixing method extracts valuable information from complex signals that cannot be resolved by standard methods. It opens new possibilities in optics and photonics for multichannel separations at an increased sampling rate.
2023-12-08
ArXiv (preprint)
arxiv.org
arxiv.org
Resolution enhancement with a task-assisted GAN to guide optical nanoscopy image analysis and acquisition
Catherine Bouchard
Theresa Wiesner
Andréanne Deschênes
Anthony Bilodeau
Benoit Turcotte
Christian Gagné
Flavie Lavoie-Cardinal
2023-07-27
Nature Machine Intelligence (published)
doi.org
Filtering Pixel Latent Variables for Unmixing Volumetric Images
Catherine Bouchard
Vincent Boulanger
Flavie Lavoie-Cardinal
Christian Gagné
Measurements of different overlapping components require robust unmixing algorithms to convert the raw multi-dimensional measurements to use… (see more)ful unmixed images. Such algorithms perform reliable separation of the components when the raw signal is fully resolved and contains enough information to fit curves on the raw distributions. In experimental physics, measurements are often noisy, undersam-pled, or unresolved spatially or spectrally. We propose a novel method where bandpass filters are applied to the latent space of a multi-dimensional convolutional neural network to separate the overlapping signal components and extract each of their relative contributions. Simultaneously processing all dimensions with multi-dimensional convolution kernels empowers the network to combine the information from adjacent pixels and time-or spectral-bins, facilitating component separation in instances where individual pixels lack well-resolved information. We demonstrate the applicability of the method to real experimental physics problems using fluorescence lifetime microscopy and mode decomposition in optical fibers as test cases. The successful application of our approach to these two distinct experimental cases, characterized by different measured distributions, highlights the versatility of our approach in addressing a wide array of imaging tasks.
2023-01-01
arXiv.org (preprint)
doi.org
Filtering Pixel Latent Variables for Unmixing Volumetric Images
Catherine Bouchard
Vincent Boulanger
Flavie Lavoie-Cardinal
Christian Gagné
Measurements of different overlapping components require robust unmixing algorithms to convert the raw multi-dimensional measurements to use… (see more)ful unmixed images. Such algorithms perform reliable separation of the components when the raw signal is fully resolved and contains enough information to fit curves on the raw distributions. In experimental physics, measurements are often noisy, undersam-pled, or unresolved spatially or spectrally. We propose a novel method where bandpass filters are applied to the latent space of a multi-dimensional convolutional neural network to separate the overlapping signal components and extract each of their relative contributions. Simultaneously processing all dimensions with multi-dimensional convolution kernels empowers the network to combine the information from adjacent pixels and time-or spectral-bins, facilitating component separation in instances where individual pixels lack well-resolved information. We demonstrate the applicability of the method to real experimental physics problems using fluorescence lifetime microscopy and mode decomposition in optical fibers as test cases. The successful application of our approach to these two distinct experimental cases, characterized by different measured distributions, highlights the versatility of our approach in addressing a wide array of imaging tasks.
2023-01-01
arXiv.org (preprint)
doi.org