Whole brain reconstruction from multilayered sections of a mouse model of status epilepticus

Liang, Haoyi; Dabrowska, Natalia; Weller, Daniel S.

doi:10.1109/acssc.2017.8335554

Cited by 2 publications

(10 citation statements)

References 15 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The proposed structure correction for brain reconstruction contains two parts: tissue flattening [32] and structure-based intensity propagation. Before tissue flattening, the structures in most layers of a multilayer section are distorted by the unevenness on zdirection.…”

Section: Proposed Structure Correction Methodsmentioning

confidence: 99%

“…Such hierarchical registration approaches are common in brain reconstruction works for the purpose of computation time and registration accuracy [18], [24]. Readers are referred to [32] for details about the implementation.…”

Section: B Alignment Pipeline In This Papermentioning

confidence: 99%

“…The tissue clearing process not only removes the lipids from the specimens, but also slightly warps the specimens. In order to process large numbers of tissues, an automatic tissue flattening method [32] is proposed. shows the detected surface layers with adaptive thresholds.…”

Section: A Flatteningmentioning

confidence: 99%

“…For this paper, multilayer sections are the raw data for whole brain reconstruction. Our previous work in [32] describes an automatic tissue flattening method to remove the warping artifacts along the cutting axis in multilayer sections. The reconstructed brains are more compact with flattened sections, but the structure inconsistence and the cylindrical artifact [28] still exist as shown in Fig.…”

Section: Introductionmentioning

confidence: 99%

“…Section II summarizes existing brain reconstruction works, and then introduces the brain registration pipeline adopted in this paper. Section III reviews the tissue flattening method in [32], and then elaborates on the proposed structure-based intensity propagation. In Section IV, experiments demonstrate how the proposed methods improve the quality of the brain reconstruction.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Structure-Based Intensity Propagation for 3-D Brain Reconstruction With Multilayer Section Microscopy

Liang

Dabrowska

Weller

2019

IEEE Trans. Med. Imaging

Self Cite

View full text Add to dashboard Cite

Microscopy is widely used for brain research because of its high resolution and ability to stain for many different biomarkers. Since whole brains are usually sectioned for tissue staining and imaging, reconstruction of 3D brain volumes from these sections is important for visualization and analysis. Recently developed tissue clearing techniques and advanced confocal microscopy enable multilayer sections to be imaged without compromising the resolution. However, noticeable structure inconsistence occurs if surface layers are used to align these sections. In this paper, a structure-based intensity propagation method is designed for the robust representation of multilayer sections. The 3D structures in reconstructed brains are more consistent using the proposed methods. Experiments are conducted on 367 multilayer sections from 20 mouse brains. The average reconstruction quality measured by the structure consistence index increases by 45% with the tissue flattening method, and 29% further with the structure-based intensity propagation.

show abstract

Section: Proposed Structure Correction Methodsmentioning

confidence: 99%