Multi-scale Image Harmonization

Traditional image compositing techniques, such as alpha matting and gradient domain compositing, are used to create composites that have plausible boundaries. But when applied to images taken from different sources or shot under different conditions, these tech- niques can produce unrealistic results. In this work, we present a framework that explicitly matches the visual appearance of images through a process we call image harmonization, before blending them. At the heart of this framework is a multi-scale technique that allows us to transfer the appearance of one image to another. We show that by carefully manipulating the scales of a pyramid decomposition of an image, we can match contrast, texture, noise, and blur, while avoiding image artifacts. The output composite can then be reconstructed from the modified pyramid coefficients while enforcing both alpha-based and seamless boundary constraints. We show how the proposed framework can be used to produce realistic composites with minimal user interaction in a number of different scenarios.Engineering and Applied Science

Scanner Invariant Representations for Diffusion MRI Harmonization

Purpose: In the present work we describe the correction of diffusion-weighted MRI for site and scanner biases using a novel method based on invariant representation. Theory and Methods: Pooled imaging data from multiple sources are subject to variation between the sources. Correcting for these biases has become very important as imaging studies increase in size and multi-site cases become more common. We propose learning an intermediate representation invariant to site/protocol variables, a technique adapted from information theory-based algorithmic fairness; by leveraging the data processing inequality, such a representation can then be used to create an image reconstruction that is uninformative of its original source, yet still faithful to underlying structures. To implement this, we use a deep learning method based on variational auto-encoders (VAE) to construct scanner invariant encodings of the imaging data. Results: To evaluate our method, we use training data from the 2018 MICCAI Computational Diffusion MRI (CDMRI) Challenge Harmonization dataset. Our proposed method shows improvements on independent test data relative to a recently published baseline method on each subtask, mapping data from three different scanning contexts to and from one separate target scanning context. Conclusion: As imaging studies continue to grow, the use of pooled multi-site imaging will similarly increase. Invariant representation presents a strong candidate for the harmonization of these data

SinDDM: A Single Image Denoising Diffusion Model

Denoising diffusion models (DDMs) have led to staggering performance leaps in image generation, editing and restoration. However, existing DDMs use very large datasets for training. Here, we introduce a framework for training a DDM on a single image. Our method, which we coin SinDDM, learns the internal statistics of the training image by using a multi-scale diffusion process. To drive the reverse diffusion process, we use a fully-convolutional light-weight denoiser, which is conditioned on both the noise level and the scale. This architecture allows generating samples of arbitrary dimensions, in a coarse-to-fine manner. As we illustrate, SinDDM generates diverse high-quality samples, and is applicable in a wide array of tasks, including style transfer and harmonization. Furthermore, it can be easily guided by external supervision. Particularly, we demonstrate text-guided generation from a single image using a pre-trained CLIP model.Comment: Improved the sampling algorith

Microscopy-BIDS: An extension to the brain imaging data structure for microscopy data

The Brain Imaging Data Structure (BIDS) is a specification for organizing, sharing, and archiving neuroimaging data and metadata in a reusable way. First developed for magnetic resonance imaging (MRI) datasets, the community-led specification evolved rapidly to include other modalities such as magnetoencephalography, positron emission tomography, and quantitative MRI (qMRI). In this work, we present an extension to BIDS for microscopy imaging data, along with example datasets. Microscopy-BIDS supports common imaging methods, including 2D/3D, ex/in vivo, micro-CT, and optical and electron microscopy. Microscopy-BIDS also includes comprehensible metadata definitions for hardware, image acquisition, and sample properties. This extension will facilitate future harmonization efforts in the context of multi-modal, multi-scale imaging such as the characterization of tissue microstructure with qMRI

Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data

The Brain Imaging Data Structure (BIDS) is a specification for organizing, sharing, and archiving neuroimaging data and metadata in a reusable way. First developed for magnetic resonance imaging (MRI) datasets, the community-led specification evolved rapidly to include other modalities such as magnetoencephalography, positron emission tomography, and quantitative MRI (qMRI). In this work, we present an extension to BIDS for microscopy imaging data, along with example datasets. Microscopy-BIDS supports common imaging methods, including 2D/3D, ex/in vivo, micro-CT, and optical and electron microscopy. Microscopy-BIDS also includes comprehensible metadata definitions for hardware, image acquisition, and sample properties. This extension will facilitate future harmonization efforts in the context of multi-modal, multi-scale imaging such as the characterization of tissue microstructure with qMRI