3D prostate histology reconstruction: an evaluation of image-based and fiducial-based algorithms

Tissue clearing and imaging approaches for in toto analysis of the reproductive system

New microscopy techniques in combination with tissue clearing protocols and emerging analytical approaches have presented researchers with the tools to understand dynamic biological processes in a three-dimensional context. This paves the road for the exploration of new research questions in reproductive biology, for which previous techniques have provided only approximate resolution. These new methodologies now allow for contextualized analysis of far larger volumes than was previously possible. Tissue optical clearing and three-dimensional imaging techniques posit the bridging of molecular mechanisms, macroscopic morphogenic development, and maintenance of reproductive function into one cohesive and comprehensive understanding of the biology of the reproductive system. In this review, we present a survey of the various tissue clearing techniques and imaging systems, as they have been applied to the developing and adult reproductive system. We provide an overview of tools available for analysis of experimental data, giving particular attention to the emergence of AI-assisted methods and their applicability to image analysis. We conclude with an evaluation of how novel image analysis approaches which have been applied to other organ systems could be incorporated into future experimental evaluation of reproductive biology.

[68Ga]Ga-PSMA and [68Ga]Ga-RM2 PET/MRI vs. Histopathological Images in Prostate Cancer: A New Workflow for Spatial Co-Registration

This study proposed a new workflow for co-registering prostate PET images from a dual-tracer PET/MRI study with histopathological images of resected prostate specimens. The method aims to establish an accurate correspondence between PET/MRI findings and histology, facilitating a deeper understanding of PET tracer distribution and enabling advanced analyses like radiomics. To achieve this, images derived by three patients who underwent both [68Ga]Ga-PSMA and [68Ga]Ga-RM2 PET/MRI before radical prostatectomy were selected. After surgery, in the resected fresh specimens, fiducial markers visible on both histology and MR images were inserted. An ex vivo MRI of the prostate served as an intermediate step for co-registration between histological specimens and in vivo MRI examinations. The co-registration workflow involved five steps, ensuring alignment between histopathological images and PET/MRI data. The target registration error (TRE) was calculated to assess the precision of the co-registration. Furthermore, the DICE score was computed between the dominant intraprostatic tumor lesions delineated by the pathologist and the nuclear medicine physician. The TRE for the co-registration of histopathology and in vivo images was 1.59 mm, while the DICE score related to the site of increased intraprostatic uptake on [68Ga]Ga-PSMA and [68Ga]Ga-RM2 PET images was 0.54 and 0.75, respectively. This work shows an accurate co-registration method for histopathological and in vivo PET/MRI prostate examinations that allows the quantitative assessment of dual-tracer PET/MRI diagnostic accuracy at a millimetric scale. This approach may unveil radiotracer uptake mechanisms and identify new PET/MRI biomarkers, thus establishing the basis for precision medicine and future analyses, such as radiomics.

Three-Dimensional Presentation of Tumor Histopathology: A Model Using Tongue Squamous Cell Carcinoma

Medical imaging often presents objects in three-dimensional (3D) form to provide better visual understanding. In contrast, histopathology is typically presented as two-dimensional (2D). Our objective was to present the tumor dimensions in 3D by creating a 3D digital model of it and so demonstrate the location of the tumor and the histological slices within the surgical soft tissue resection specimen. We developed a novel method for modeling a tongue squamous cell carcinoma using commonly available instruments. We established our 3D-modeling method by recognizing and solving challenges that concern the selection of the direction of histological slices. Additional steps to standard handling included scanning the specimen prior to grossing and modeling the carcinoma, which required only a table scanner and modeling software. We present challenges and their solutions in modeling the resection specimen and its histological slices. We introduce a finished 3D model of a soft tissue resection specimen and the actual tumor as well as its histopathological grossing sites in 3D digital and printed form. Our novel method provides steps to create a digital model of soft tissue resection specimen and the tumor within. To our knowledge, this is the first attempt to present histopathological margins of a tongue tumor in 3D form, whereas previously, only 2D has been available. The creation of the 3D model does not call for predetermined grossing directions for the pathologist. In addition, it provides a crucial initiative to enhance oncological management. The method allows a better visual understanding of tumor margins, topography, and orientation. It thus provides a tool for an improved postoperative assessment and aids, for example, in the discussion of the need for additional surgery and adjuvant therapy.

A system using patient-specific 3D-printed molds to spatially align in vivo MRI with ex vivo MRI and whole-mount histopathology for prostate cancer research

BACKGROUND

Patient-specific 3D-printed molds and ex vivo MRI of the resected prostate have been two important strategies to align MRI with whole-mount histopathology (WMHP) for prostate cancer (PCa) research, but the combination of these two strategies has not been systematically evaluated.

PURPOSE

To develop and evaluate a system that combines patient-specific 3D-printed molds with ex vivo MRI (ExV) to spatially align in vivo MRI (InV), ExV, and WMHP in PCa patients.

STUDY TYPE

Prospective cohort study.

POPULATION

Seventeen PCa patients who underwent 3T MRI and robotic-assisted laparoscopic radical prostatectomy (RALP).

FIELD STRENGTH/SEQUENCES

T₂ -weighted turbo spin-echo sequences at 3T.

ASSESSMENT

Immediately after RALP, the fresh whole prostate specimens were imaged in patient-specific 3D-printed molds by 3T MRI and then sectioned to create WMHP slides. The time required for ExV was measured to assess impact on workflow. InV, ExV, and WMHP images were registered. Spatial alignment was evaluated using: slide offset (mm) between ExV slice locations and WMHP slides; overlap of the 3D prostate contour on InV versus ExV using Dice's coefficient (0 to 1); and 2D target registration error (TRE, mm) between corresponding landmarks on InV, ExV, and WMHP. Data are reported as mean ± standard deviation (SD).

STATISTICAL TESTING

Differences in 2D TRE before versus after registration were compared using the Wilcoxon signed-rank test (P < 0.05 considered significant).

RESULTS

ExV (duration 115 ± 15 min) was successfully incorporated into the workflow for all cases. Absolute slide offset was 1.58 ± 1.57 mm. Dice's coefficient was 0.865 ± 0.035. 2D TRE was significantly reduced after registration (P < 0.01) with mean (±SD of per patient means) of 1.9 ± 0.6 mm for InV versus ExV, 1.4 ± 0.5 mm for WMHP versus ExV, and 2.0 ± 0.5 mm for WMHP versus InV.

DATA CONCLUSION

The proposed system combines patient-specific 3D-printed molds with ExV to achieve spatial alignment between InV, ExV, and WMHP with mean 2D TRE of 1-2 mm.

LEVEL OF EVIDENCE

2 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2019;49:270-279.

Quantified analysis of histological components and architectural patterns of gleason grades in apparent diffusion coefficient restricted areas upon diffusion weighted MRI for peripheral or transition zone cancer locations

PURPOSE

To quantify and compare the histological components and architectural patterns of Gleason grades in cancerous areas with restriction on apparent diffusion coefficient (ADC) maps.

MATERIALS AND METHODS

Twelve consecutive cases with 14 separate ADC restriction areas, positive for cancer in the peripheral zone (PZ) and transition zone (TZ) were included. All had 3 Tesla MRI and radical prostatectomy. Ten regions of interest (ROIs) within and outside the 14 ADC restriction areas positive for cancer were selected. For each ROI, we performed quantitative analysis of (a) prostate benign and malignant histological component surface ratios, including stroma, glands, epithelium, lumen, cellular nuclei; (b) percent of Gleason grades and measures of ADC values. Means of histological components according to ADC restriction for cancerous area were compared with analyses of variance with repeated measures.

RESULTS

Independent predictors of the probability of cancer were median epithelium/ROI ratio (P = 0.001) and nuclei/ROI ratio (P = 0.03). Independent predictors of the probability of ADC restriction were malignant glands/ROI and luminal space/ROI (P < 0.0001). Effect of malignant glands/ROI area was different according to the localization of the ROI (P = 0.03). We observed an overall difference between the means for all of the histological components for the comparison of true positive and false negative (P < 0.0001), except for the percent of Gleason grade 4 (P = 0.18). In TZ cancers, a predominant grade 3 pattern was associated with low ADC values. In PZ cancers, a predominant grade 4 pattern was associated with low ADC values.

CONCLUSION

Determinants of low ADC were high ratio of malignant glands/ROI area which may be seen in Gleason grades 3 or 4 cancers.

LEVEL OF EVIDENCE

3 Technical Efficacy: Stage 3 J. Magn. Reson. Imaging 2017;46:1786-1796.

Optimized SIFTFlow for registration of whole-mount histology to reference optical images

The registration of two-dimensional histology images to reference images from other modalities is an important preprocessing step in the reconstruction of three-dimensional histology volumes. This is a challenging problem because of the differences in the appearances of histology images and other modalities, and the presence of large nonrigid deformations which occur during slide preparation. This paper shows the feasibility of using densely sampled scale-invariant feature transform (SIFT) features and a SIFTFlow deformable registration algorithm for coregistering whole-mount histology images with blockface optical images. We present a method for jointly optimizing the regularization parameters used by the SIFTFlow objective function and use it to determine the most appropriate values for the registration of breast lumpectomy specimens. We demonstrate that tuning the regularization parameters results in significant improvements in accuracy and we also show that SIFTFlow outperforms a previously described edge-based registration method. The accuracy of the histology images to blockface images registration using the optimized SIFTFlow method was assessed using an independent test set of images from five different lumpectomy specimens and the mean registration error was [Formula: see text].

Computer-aided Detection of Prostate Cancer with MRI: Technology and Applications

One in six men will develop prostate cancer in his lifetime. Early detection and accurate diagnosis of the disease can improve cancer survival and reduce treatment costs. Recently, imaging of prostate cancer has greatly advanced since the introduction of multiparametric magnetic resonance imaging (mp-MRI). Mp-MRI consists of T2-weighted sequences combined with functional sequences including dynamic contrast-enhanced MRI, diffusion-weighted MRI, and magnetic resonance spectroscopy imaging. Because of the big data and variations in imaging sequences, detection can be affected by multiple factors such as observer variability and visibility and complexity of the lesions. To improve quantitative assessment of the disease, various computer-aided detection systems have been designed to help radiologists in their clinical practice. This review paper presents an overview of literatures on computer-aided detection of prostate cancer with mp-MRI, which include the technology and its applications. The aim of the survey is threefold: an introduction for those new to the field, an overview for those working in the field, and a reference for those searching for literature on a specific application.

The Role of Micro-CT in 3D Histology Imaging

OBJECTIVES

3D histology tissue modeling is a useful analytical technique for understanding anatomy and disease at the cellular level. However, the current accuracy of 3D histology technology is largely unknown, and errors, misalignment and missing information are common in 3D tissue reconstruction. We used micro-CT imaging technology to better understand these issues and the relationship between fresh tissue and its 3D histology counterpart.

METHODS

We imaged formalin-fixed and 2% Lugol-stained mouse brain, human uterus and human lung tissue with micro-CT. We then conducted image analyses on the tissues before and after paraffin embedding using 3D Slicer and ImageJ software to understand how tissue changes between the fixation and embedding steps.

RESULTS

We found that all tissue samples decreased in volume by 19.2-61.5% after embedding, that micro-CT imaging can be used to assess the integrity of tissue blocks, and that micro-CT analysis can help to design an optimized tissue-sectioning protocol.

CONCLUSIONS

Micro-CT reference data help to identify where and to what extent tissue was lost or damaged during slide production, provides valuable anatomical information for reconstructing missing parts of a 3D tissue model, and aids in correcting reconstruction errors when fitting the image information in vivo and ex vivo.

3D surface-based registration of ultrasound and histology in prostate cancer imaging

Several transrectal ultrasound (TRUS)-based techniques aiming at accurate localization of prostate cancer are emerging to improve diagnostics or to assist with focal therapy. However, precise validation prior to introduction into clinical practice is required. Histopathology after radical prostatectomy provides an excellent ground truth, but needs accurate registration with imaging. In this work, a 3D, surface-based, elastic registration method was developed to fuse TRUS images with histopathologic results. To maximize the applicability in clinical practice, no auxiliary sensors or dedicated hardware were used for the registration. The mean registration errors, measured in vitro and in vivo, were 1.5±0.2 and 2.1±0.5mm, respectively.

A Method for 3D Histopathology Reconstruction Supporting Mouse Microvasculature Analysis

Structural abnormalities of the microvasculature can impair perfusion and function. Conventional histology provides good spatial resolution with which to evaluate the microvascular structure but affords no 3-dimensional information; this limitation could lead to misinterpretations of the complex microvessel network in health and disease. The objective of this study was to develop and evaluate an accurate, fully automated 3D histology reconstruction method to visualize the arterioles and venules within the mouse hind-limb. Sections of the tibialis anterior muscle from C57BL/J6 mice (both normal and subjected to femoral artery excision) were reconstructed using pairwise rigid and affine registrations of 5 µm-thick, paraffin-embedded serial sections digitized at 0.25 µm/pixel. Low-resolution intensity-based rigid registration was used to initialize the nucleus landmark-based registration, and conventional high-resolution intensity-based registration method. The affine nucleus landmark-based registration was developed in this work and was compared to the conventional affine high-resolution intensity-based registration method. Target registration errors were measured between adjacent tissue sections (pairwise error), as well as with respect to a 3D reference reconstruction (accumulated error, to capture propagation of error through the stack of sections). Accumulated error measures were lower (p < 0.01) for the nucleus landmark technique and superior vasculature continuity was observed. These findings indicate that registration based on automatic extraction and correspondence of small, homologous landmarks may support accurate 3D histology reconstruction. This technique avoids the otherwise problematic "banana-into-cylinder" effect observed using conventional methods that optimize the pairwise alignment of salient structures, forcing them to be section-orthogonal. This approach will provide a valuable tool for high-accuracy 3D histology tissue reconstructions for analysis of diseased microvasculature.

Computer-assisted three-dimensional analysis of multifocal/multicentric prostate cancer

In order to study multiple contiguous prostate cancer lesions, we constructed computer-assisted, three-dimensional models of multifocal prostate cancer specimens obtained by radical prostatectomy. We then examined the genetic heterogeneity among the specimens by DNA microarray analysis. Cancer foci with high Gleason patterns were found to occur de novo, whereas those with low Gleason patterns occurred contiguously with cancers of low Gleason patterns. Three-dimensional analysis showed that distinct, noncontiguous cancerous foci were genetically independent and multicentric. In contrast some contiguous multifocal lesions had the same genetic origin.