BIRL: Benchmark on Image Registration methods with Landmark validation (2019-12-31T00:00:00.000000Z)

TL;DR

A generic image registration benchmark with automatic evaluation using landmark annotations, an integration of several standard image registration methods aiming at biomedical imaging into the BIRL framework, and experimental results of these SOTA methods on the CIMA dataset.

Abstract

This report presents a generic image registration benchmark with automatic evaluation using landmark annotations. The key features of the BIRL framework are: easily extendable, performance evaluation, parallel experimentation, simple visualisations, experiment's time-out limit, resuming unfinished experiments. From the research practice, we identified and focused on these two main use-cases: (a) comparison of user's (newly developed) method with some State-of-the-Art (SOTA) methods on a common dataset and (b) experimenting SOTA methods on user's custom dataset (which should contain landmark annotation). Moreover, we present an integration of several standard image registration methods aiming at biomedical imaging into the BIRL framework. This report also contains experimental results of these SOTA methods on the CIMA dataset, which is a dataset of Whole Slice Imaging (WSI) from histology/pathology containing several multi-stain tissue samples from three tissue kinds. Source and results: this https URL

Authors

Jiri Borovec

2 papers

TL;DR

Abstract

Authors

References39 items

The Continuous Registration Challenge: Evaluation-as-a-Service for Medical Image Registration Algorithms

Deep learning in medical image registration: a survey

Challenges and Solutions in Multimodal Medical Image Subregion Detection and Registration.

Benchmarking of Image Registration Methods for Differently Stained Histological Slides

Comparative analysis of tissue reconstruction algorithms for 3D histology

The human protein atlas: A spatial map of the human proteome

AN INVESTIGATION TOWARDS ISSUES AND CHALLENGES IN MEDICAL IMAGE REGISTRATION

Multi-stained whole slide image alignment in digital pathology

Automatic simultaneous segmentation and fast registration of histological images

Comparative Evaluation of Registration Algorithms in Different Brain Databases With Varying Difficulty: Results and Insights

A symmetric block-matching framework for global registration

Deformable Medical Image Registration: A Survey

Registration of multiple stained histological sections

Survey of Medical Image Registration

3D reconstruction of multiple stained histology images

Fiji: an open-source platform for biological-image analysis

The interstitial expression of alpha-smooth muscle actin in glomerulonephritis is associated with renal function

Development of Multigene Expression Signature Maps at the Protein Level from Digitized Immunohistochemistry Slides

Deformable medical image registration: setting the state of the art with discrete methods.

Evaluation of Registration Methods on Thoracic CT: The EMPIRE10 Challenge

Expression of the neuron-specific protein CHD5 is an independent marker of outcome in neuroblastoma

Results of a multi-institution deformable registration accuracy study (MIDRAS).

Histopathological Image Analysis: A Review

Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration

A framework for evaluation of deformable image registration spatial accuracy using large landmark point sets

Dense image registration through MRFs and efficient linear programming

Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain

A genome-scale map of expression for a mouse brain section obtained using voxelation.

A review of recent range image registration methods with accuracy evaluation

Introduction to the Non-rigid Image Registration Evaluation Project (NIREP)

Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization

Distinctive Image Features from Scale-Invariant Keypoints

Image registration methods: a survey

Comparison and evaluation of retrospective intermodality brain image registration techniques.

Registration of whole immunohistochemical slide images: an efficient way to characterize biomarker colocalization

Distinctive Image Features from Scale-Invariant Keypoints Abstract by Matthijs Dorst Based on the paper by

elastix: A Toolbox for Intensity-Based Medical Image Registration

A System for Combined Three-Dimensional Morphological and Molecular Analysis of Thick Tissue Specimens

Reconstructing a 3D structure from serial histological sections

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