A low temperature embedding and section registration strategy for 3D image reconstruction of the rat brain from autoradiographic sections

Simonetti, Arjan W.; Elezi, Vedat A.; Farion, Régine; Malandain, Grégoire; Segebarth, Christoph; Rémy, Chantal; Barbier, Emmanuel

doi:10.1016/j.jneumeth.2006.06.004

Cited by 14 publications

(12 citation statements)

References 22 publications

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“…This issue is bypassed in Refs. (Simonetti et al, 2006;Streicher et al, 1997), where four markers are inserted perpendicular to the chuck onto which the brain tissue is glued and not through the tissue itself. Yet, if the needles are not parallel to the cutting axis, or if the needle holes collapse, this approach may still produce an inaccurate reconstructed volume.…”

Section: -D Reconstruction Using 2-d/2-d Registration Of Histologicamentioning

confidence: 99%

Smoothness-guided 3-D reconstruction of 2-D histological images

Cifor

Pitiot

2011

NeuroImage

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Section: -D Reconstruction Using 2-d/2-d Registration Of Histologicamentioning

confidence: 99%

Smoothness-guided 3-D reconstruction of 2-D histological images

Cifor

Pitiot

2011

NeuroImage

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“…Several techniques have previously been employed to automatically align sections. These include fiducial markers based on needle or drill holes, tubes and tissue array cores (Bussolati et al, 2005;Dogdas et al, 2007;Goldszal et al, 1995;Simonetti et al, 2006;Streicher et al, 1997) as well as approaches that exploit tissue content information from adjacent slices (Cohen et al, 1998;Ju et al, 2006;Ourselin et al, 2001b) or different image sources (Dauguet et al, 2007;LONI, 2006).…”

Section: Introductionmentioning

confidence: 99%

An assessment of methods for aligning two-dimensional microscope sections to create image volumes

Beare

Richards

Murphy

et al. 2008

Journal of Neuroscience Methods

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“…2A), which was similar to a previously reported prototype [16]. Specifically, 4 parallel holes were drilled in two rigid plastic plates (6 mm thickness).…”

Section: Methodsmentioning

confidence: 78%

An alternative approach to histopathological validation of PET imaging for radiation therapy image-guidance: A proof of concept

Axente

Bass

et al. 2014

Radiotherapy and Oncology

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Purpose In radiotherapy, PET images can be used to guide the delivery of selectively escalated doses to biologically relevant tumour subvolumes. Validation of PET for such applications requires demonstration of spatial coincidence between PET tracer uptake pattern and the histopathologically confirmed target. This study introduces a novel approach to histopathological validation of PET image segmentation for radiotherapy guidance. Methods and materials Sequential tissue sections from surgically excised whole-tumour specimens were used to acquire full 3D-sets of both histopathological images (microscopy) and PET tracer distribution images (autoradiography). After these datasets were accurately registered, a full 3D autoradiographic distribution of PET tracer was reconstructed and used to obtain synthetic PET images (sPET) by simulating the image deterioration induced by processes involved in PET image formation. To illustrate the method, sPET images were used in this study to investigate spatial coincidence between high FDG uptake areas and the distribution of viable tissue in two small animal tumour models. Results The reconstructed 3D autoradiographic distribution of the PET tracer was spatially coherent, as indicated by the high average value of the pised pixel-by-pixel correlation of intensities between successive slices (0.84 ± 0.05 and 0.94 ± 0.02). The loss of detail in the sPET images versus the 3D autoradiography was significant as indicated by Dice coefficient values corresponding to the two tumours (0 and 0.1 at 70% threshold). The maximum overlap between the FDG segmented volumes and the extent of the viable tissue as indicated by Dice coefficient values, was 0.8 for one tumour (for the image thresholded at 22% of max intensity) and 0.88 for the other (threshold of 14% of max intensity). Conclusion It was demonstrated that the use of synthetic PET images for histopathological validation allows for bypassing a technically challenging and error-prone step of registering non-invasive PET images with histopathology.

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A low temperature embedding and section registration strategy for 3D image reconstruction of the rat brain from autoradiographic sections

Cited by 14 publications

References 22 publications

Smoothness-guided 3-D reconstruction of 2-D histological images

Smoothness-guided 3-D reconstruction of 2-D histological images

An assessment of methods for aligning two-dimensional microscope sections to create image volumes

An alternative approach to histopathological validation of PET imaging for radiation therapy image-guidance: A proof of concept

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