Regional Registration of Whole Slide Image Stacks Containing Highly Deformed Artefacts

Abstract Background: High resolution 2D whole slide imaging provides rich information about the tissue structure. This information can be a lot richer if these 2D images can be stacked into a 3D tissue volume. A 3D analysis, however, requires accurate reconstruction of the tissue volume from the 2D image stack. This task is not trivial due to the distortions that each individual tissue slice experiences while cutting and mounting the tissue on the glass slide. Performing registration for the whole tissue slices may be adversely affected by the deformed tissue regions. Consequently, regional registration is found to be more effective. In this paper, we propose an accurate and robust regional registration algorithm for whole slide images which incrementally focuses registration on the area around the region of interest. Results: Using mean similarity index as the metric, the proposed algorithm (mean +- std: 0.84 +- 0.11) followed by a fine registration algorithm (0.86 +- 0.08) outperformed the state-of-the-art linear whole tissue registration algorithm (0.74 +- 0.19) and the regional version of this algorithm (0.81 +- 0.15). The proposed algorithm also outperforms the state-of-the-art nonlinear registration algorithm (original: 0.82 +- 0.12, regional: 0.77 +- 0.22) for whole slide images and a recently proposed patch-based registration algorithm (patch size 256: 0.79 +- 0.16 , patch size 512: 0.77 +- 0.16) for medical images. Conclusion: The proposed algorithm is a more robust and accurate solution to the problem of regional registration of whole slide images in existence of highly deformed regions in the imaged tissue.

Download Full-text

Regional Registration of Whole Slide Image Stacks Containing Major Histological Artifacts

10.21203/rs.3.rs-17938/v3 ◽

2020 ◽

Author(s):

Mahsa Paknezhad ◽

Sheng Yang Michael Loh ◽

Yukti Choudhury ◽

Valerie Koh Cui Koh ◽

Timothy Tay Kwang Yong ◽

...

Keyword(s):

Patch Size ◽

State Of The Art ◽

The State ◽

3D Analysis ◽

Image Stack ◽

Tissue Volume ◽

Multi Scale ◽

Registration Algorithm ◽

Regional Registration ◽

Whole Slide Images

Abstract Background: High resolution 2D whole slide imaging provides rich information about the tissue structure. This information can be a lot richer if these 2D images can be stacked into a 3D tissue volume. A 3D analysis, however, requires accurate reconstruction of the tissue volume from the 2D image stack. This task is not trivial due to the distortions such as tissue tearing, folding and missing at each slide. Performing registration for the whole tissue slices may be adversely affected by distorted tissue regions. Consequently, regional registration is found to be more effective. In this paper, we propose a new approach to an accurate and robust registration of regions of interest for whole slide images. We introduce the idea of multi-scale attention for registration. Results: Using mean similarity index as the metric, the proposed algorithm (mean +- std: 0.84 +- 0.11) followed by a fine registration algorithm (0.86 +- 0.08) outperformed the state-of-the-art linear whole tissue registration algorithm (0.74 +- 0.19) and the regional version of this algorithm (0.81 +- 0.15). The proposed algorithm also outperforms the state-of-the-art nonlinear registration algorithm (original: 0.82 +- 0.12, regional: 0.77 +- 0.22) for whole slide images and a recently proposed patch-based registration algorithm (patch size 256: 0.79 +- 0.16 , patch size 512: 0.77 +- 0.16) for medical images. Conclusion: Using multi-scale attention mechanism leads to a more robust and accurate solution to the problem of regional registration of whole slide images corrupted in some parts by major histological artifacts in the imaged tissue.

Download Full-text

Regional registration of whole slide image stacks containing major histological artifacts

BMC Bioinformatics ◽

10.1186/s12859-020-03907-6 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Mahsa Paknezhad ◽

Sheng Yang Michael Loh ◽

Yukti Choudhury ◽

Valerie Koh Cui Koh ◽

Timothy Tay Kwang Yong ◽

...

Keyword(s):

Patch Size ◽

State Of The Art ◽

The State ◽

3D Analysis ◽

Image Stack ◽

Tissue Volume ◽

Multi Scale ◽

Registration Algorithm ◽

Regional Registration ◽

Whole Slide Images

Abstract Background High resolution 2D whole slide imaging provides rich information about the tissue structure. This information can be a lot richer if these 2D images can be stacked into a 3D tissue volume. A 3D analysis, however, requires accurate reconstruction of the tissue volume from the 2D image stack. This task is not trivial due to the distortions such as tissue tearing, folding and missing at each slide. Performing registration for the whole tissue slices may be adversely affected by distorted tissue regions. Consequently, regional registration is found to be more effective. In this paper, we propose a new approach to an accurate and robust registration of regions of interest for whole slide images. We introduce the idea of multi-scale attention for registration. Results Using mean similarity index as the metric, the proposed algorithm (mean ± SD $$0.84 \pm 0.11$$ 0.84 ± 0.11 ) followed by a fine registration algorithm ($$0.86 \pm 0.08$$ 0.86 ± 0.08 ) outperformed the state-of-the-art linear whole tissue registration algorithm ($$0.74 \pm 0.19$$ 0.74 ± 0.19 ) and the regional version of this algorithm ($$0.81 \pm 0.15$$ 0.81 ± 0.15 ). The proposed algorithm also outperforms the state-of-the-art nonlinear registration algorithm (original: $$0.82 \pm 0.12$$ 0.82 ± 0.12 , regional: $$0.77 \pm 0.22$$ 0.77 ± 0.22 ) for whole slide images and a recently proposed patch-based registration algorithm (patch size 256: $$0.79 \pm 0.16$$ 0.79 ± 0.16 , patch size 512: $$0.77 \pm 0.16$$ 0.77 ± 0.16 ) for medical images. Conclusion Using multi-scale attention mechanism leads to a more robust and accurate solution to the problem of regional registration of whole slide images corrupted in some parts by major histological artifacts in the imaged tissue.

Download Full-text

Regional Registration of Whole Slide Image Stacks Containing Major Histological Artifacts

10.21203/rs.3.rs-17938/v2 ◽

2020 ◽

Author(s):

Mahsa Paknezhad ◽

Sheng Yang Michael Loh ◽

Yukti Choudhury ◽

Valerie Koh Cui Koh ◽

Timothy Tay Kwang Yong ◽

...

Keyword(s):

Patch Size ◽

State Of The Art ◽

The State ◽

3D Analysis ◽

Image Stack ◽

Tissue Volume ◽

Multi Scale ◽

Registration Algorithm ◽

Regional Registration ◽

Whole Slide Images

Abstract Background: High resolution 2D whole slide imaging provides rich information about the tissue structure. This information can be a lot richer if these 2D images can be stacked into a 3D tissue volume. A 3D analysis, however, requires accurate reconstruction of the tissue volume from the 2D image stack. This task is not trivial due to the distortions such as tissue tearing, folding and missing at each slide. Performing registration for the whole tissue slices may be adversely affected by distorted tissue regions. Consequently, regional registration is found to be more effective. In this paper, we propose a new approach to an accurate and robust registration of regions of interest for whole slide images. We introduce the idea of multi-scale attention for registration. Results: Using mean similarity index as the metric, the proposed algorithm (mean +- std: 0.84 +- 0.11) followed by a fine registration algorithm (0.86 +- 0.08) outperformed the state-of-the-art linear whole tissue registration algorithm (0.74 +- 0.19) and the regional version of this algorithm (0.81 +- 0.15). The proposed algorithm also outperforms the state-of-the-art nonlinear registration algorithm (original: 0.82 +- 0.12, regional: 0.77 +- 0.22) for whole slide images and a recently proposed patch-based registration algorithm (patch size 256: 0.79 +- 0.16 , patch size 512: 0.77 +- 0.16) for medical images. Conclusion: Using multi-scale attention mechanism leads to a more robust and accurate solution to the problem of regional registration of whole slide images corrupted in some parts by major histological artifacts in the imaged tissue.

Download Full-text

Practical Picture Processing

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100051700 ◽

1974 ◽

Vol 32 ◽

pp. 338-339

Author(s):

T. A. Welton

Keyword(s):

Radiation Damage ◽

Coherence Length ◽

Spatial Information ◽

State Of The Art ◽

Coherent Radiation ◽

The State ◽

Energy Spread ◽

Electron Micrograph ◽

Picture Processing ◽

Molecular Skeleton

Various authors have emphasized the spatial information resident in an electron micrograph taken with adequately coherent radiation. In view of the completion of at least one such instrument, this opportunity is taken to summarize the state of the art of processing such micrographs. We use the usual symbols for the aberration coefficients, and supplement these with £ and 6 for the transverse coherence length and the fractional energy spread respectively. He also assume a weak, biologically interesting sample, with principal interest lying in the molecular skeleton remaining after obvious hydrogen loss and other radiation damage has occurred.

Download Full-text