CLAIRE – Parallelized Diffeomorphic Image Registration for Large-Scale Biomedical Imaging Applications

by   Naveen Himthani, et al.

We study the performance of CLAIRE – a diffeomorphic multi-node, multi-GPU image-registration algorithm, and software – in large-scale biomedical imaging applications with billions of voxels. At such resolutions, most existing software packages for diffeomorphic image registration are prohibitively expensive. As a result, practitioners first significantly downsample the original images and then register them using existing tools. Our main contribution is an extensive analysis of the impact of downsampling on registration performance. We study this impact by comparing full-resolution registrations obtained with CLAIRE to lower-resolution registrations for synthetic and real-world imaging datasets. Our results suggest that registration at full resolution can yield a superior registration quality – but not always. For example, downsampling a synthetic image from 1024^3 to 256^3 decreases the Dice coefficient from 92 differences are less pronounced for noisy or low-contrast high-resolution images. CLAIRE allows us not only to register images of clinically relevant size in a few seconds but also to register images at unprecedented resolution in a reasonable time. The highest resolution considered is CLARITY images of size 2816×3016×1162. To the best of our knowledge, this is the first study on image registration quality at such resolutions.


page 3

page 15

page 16

page 17

page 21

page 23

page 26


Performance of Image Registration Tools on High-Resolution 3D Brain Images

Recent progress in tissue clearing has allowed for the imaging of entire...

MDReg-Net: Multi-resolution diffeomorphic image registration using fully convolutional networks with deep self-supervision

We present a diffeomorphic image registration algorithm to learn spatial...

TRIM: Triangulating Images for Efficient Registration

With the advancement in the digital camera technology, the use of high r...

Multi-Node Multi-GPU Diffeomorphic Image Registration for Large-Scale Imaging Problems

We present a Gauss-Newton-Krylov solver for large deformation diffeomorp...

Work-stealing prefix scan: Addressing load imbalance in large-scale image registration

Parallelism patterns (e.g., map or reduce) have proven to be effective t...

Towards ultra-high resolution 3D reconstruction of a whole rat brain from 3D-PLI data

3D reconstruction of the fiber connectivity of the rat brain at microsco...

Scale-arbitrary Invertible Image Downscaling

Downscaling is indispensable when distributing high-resolution (HR) imag...

Please sign up or login with your details

Forgot password? Click here to reset