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J.M.J. van Beurden
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Bridging the Gap: Semi-Automated 3D Histopathology-to-Ultrasound Registration
Towards Intraoperative Margin Assessment in Oral Cancer Surgery
Master thesis
(2026)
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J.M.J. van Beurden, Theo van Walsum, Maarten van Alphen, Luc Karssemakers, Andrea Borghesi, Lotje Zuur
Introduction: Surgical resection is the primary treatment for tongue squamous cell carcinoma (TSCC), but inadequate margins occur in up to 85\% of cases in Dutch cohorts. Histopathology is the gold standard for margin assessment, but its result only becomes available days after surgery, leaving the surgeon without intra-operative feedback. A deep learning model segmenting the tumour in ex-vivo 3D ultrasound (US) could give intra-operative feedback, but needs training labels with a known tumour boundary in US space. Histopathology provides that boundary in a separate coordinate system, so transferring it requires image registration.
Methods: A semi-automated 3D-to-3D registration pipeline was developed for oral-cavity specimens. A 3D histopathology volume is reconstructed from serial 2D H\&E slices, refined per slice using internal fiducial needles, and registered as a whole to the 3D US volume, held as the fixed reference. Registration estimates similarity transforms by aligning the specimen boundaries through signed distance fields. The pipeline was validated on a development and a held-out cohort without parameter re-tuning, using fiducial TRE, landmark TRE, NSD@1mm, and Dice; individual components were assessed through ablation and sensitivity experiments.
Results: On the development cohort ($n=5$), the pipeline reached a mean fiducial TRE of 1.56~mm, a mean landmark TRE of 1.69~mm, an NSD@1mm of 0.89, and a whole-specimen Dice of 0.80. On the held-out cohort ($n=7$), accuracy remained in similar range (2.13~mm, 2.23~mm, 0.87, 0.74).
Conclusion: To our knowledge, this is the first pipeline to register a reconstructed 3D histopathology volume to 3D US for oral-cavity specimens, with slice correspondence recovered semi-automatically rather than fixed by hand for each specimen. The current accuracy of roughly 2~mm limits direct margin assessment at the 1~mm threshold, but provides a scalable framework and an accuracy baseline for generating registered training data. ...
Methods: A semi-automated 3D-to-3D registration pipeline was developed for oral-cavity specimens. A 3D histopathology volume is reconstructed from serial 2D H\&E slices, refined per slice using internal fiducial needles, and registered as a whole to the 3D US volume, held as the fixed reference. Registration estimates similarity transforms by aligning the specimen boundaries through signed distance fields. The pipeline was validated on a development and a held-out cohort without parameter re-tuning, using fiducial TRE, landmark TRE, NSD@1mm, and Dice; individual components were assessed through ablation and sensitivity experiments.
Results: On the development cohort ($n=5$), the pipeline reached a mean fiducial TRE of 1.56~mm, a mean landmark TRE of 1.69~mm, an NSD@1mm of 0.89, and a whole-specimen Dice of 0.80. On the held-out cohort ($n=7$), accuracy remained in similar range (2.13~mm, 2.23~mm, 0.87, 0.74).
Conclusion: To our knowledge, this is the first pipeline to register a reconstructed 3D histopathology volume to 3D US for oral-cavity specimens, with slice correspondence recovered semi-automatically rather than fixed by hand for each specimen. The current accuracy of roughly 2~mm limits direct margin assessment at the 1~mm threshold, but provides a scalable framework and an accuracy baseline for generating registered training data. ...
Introduction: Surgical resection is the primary treatment for tongue squamous cell carcinoma (TSCC), but inadequate margins occur in up to 85\% of cases in Dutch cohorts. Histopathology is the gold standard for margin assessment, but its result only becomes available days after surgery, leaving the surgeon without intra-operative feedback. A deep learning model segmenting the tumour in ex-vivo 3D ultrasound (US) could give intra-operative feedback, but needs training labels with a known tumour boundary in US space. Histopathology provides that boundary in a separate coordinate system, so transferring it requires image registration.
Methods: A semi-automated 3D-to-3D registration pipeline was developed for oral-cavity specimens. A 3D histopathology volume is reconstructed from serial 2D H\&E slices, refined per slice using internal fiducial needles, and registered as a whole to the 3D US volume, held as the fixed reference. Registration estimates similarity transforms by aligning the specimen boundaries through signed distance fields. The pipeline was validated on a development and a held-out cohort without parameter re-tuning, using fiducial TRE, landmark TRE, NSD@1mm, and Dice; individual components were assessed through ablation and sensitivity experiments.
Results: On the development cohort ($n=5$), the pipeline reached a mean fiducial TRE of 1.56~mm, a mean landmark TRE of 1.69~mm, an NSD@1mm of 0.89, and a whole-specimen Dice of 0.80. On the held-out cohort ($n=7$), accuracy remained in similar range (2.13~mm, 2.23~mm, 0.87, 0.74).
Conclusion: To our knowledge, this is the first pipeline to register a reconstructed 3D histopathology volume to 3D US for oral-cavity specimens, with slice correspondence recovered semi-automatically rather than fixed by hand for each specimen. The current accuracy of roughly 2~mm limits direct margin assessment at the 1~mm threshold, but provides a scalable framework and an accuracy baseline for generating registered training data.
Methods: A semi-automated 3D-to-3D registration pipeline was developed for oral-cavity specimens. A 3D histopathology volume is reconstructed from serial 2D H\&E slices, refined per slice using internal fiducial needles, and registered as a whole to the 3D US volume, held as the fixed reference. Registration estimates similarity transforms by aligning the specimen boundaries through signed distance fields. The pipeline was validated on a development and a held-out cohort without parameter re-tuning, using fiducial TRE, landmark TRE, NSD@1mm, and Dice; individual components were assessed through ablation and sensitivity experiments.
Results: On the development cohort ($n=5$), the pipeline reached a mean fiducial TRE of 1.56~mm, a mean landmark TRE of 1.69~mm, an NSD@1mm of 0.89, and a whole-specimen Dice of 0.80. On the held-out cohort ($n=7$), accuracy remained in similar range (2.13~mm, 2.23~mm, 0.87, 0.74).
Conclusion: To our knowledge, this is the first pipeline to register a reconstructed 3D histopathology volume to 3D US for oral-cavity specimens, with slice correspondence recovered semi-automatically rather than fixed by hand for each specimen. The current accuracy of roughly 2~mm limits direct margin assessment at the 1~mm threshold, but provides a scalable framework and an accuracy baseline for generating registered training data.
Student report
(2025)
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Sophie ten Hoor, Olivier Stades, Julia van Beurden, Jelle Rigter, Anahí Witzenburg, Floor Dijkstra, S.C. Santema, J.S. Hoving, José A. Á. Antolínez, A.T. Gebremariam, J. Dankelman, M. Walraven
The Port of Santa Fe was once a major hub for both domestic and international trade, but changing river dynamics have reduced its accessibility and economic importance. As a result, the port now faces the challenge of redefining its role and exploring new functions that reconnect the port with the public. The Dyke 2 waterfront in the Port of Santa Fe, is currently in a deteriorated and underdeveloped state, lacking essential public facilities, accessible green spaces, and safe access to the river. Most importantly, the site faces severe riverbank instability, confirmed by a calculated Safety Factor (SF) of 0.67.
This report presents an integrated vision and technical design for the sustainable redevelopment of the project site area, commissioned as an advisory document for the Ente Administrador del Puerto de Santa Fe (EAPSF). The project employed a strategic track, guided by four pillars, and a slope protection track, using a Multi-Criteria Decision Analysis (MCDA) to select a solution, resulting in a design containing both technical stability and a public urban concept.
The resulting urban concept, The Santa Fe Riverside Park, serves as a project embodying the strategic vision. The design integrates adaptive infrastructure, including stepped terraces and docking places, engineered to accommodate significant seasonal river fluctuations. This concept is supported by the delivery of a 15-year long-term roadmap. The unstable slope is protected using an ecosystem-friendly Articulated Concrete Block mattress system, improving the calculated sliding SF from 0.67 to 1.9, and achieving an erosion SF of 2.10.
Finally, the report provides the Port Authority with a strategic foundation of recommendations to realise the project.
...
This report presents an integrated vision and technical design for the sustainable redevelopment of the project site area, commissioned as an advisory document for the Ente Administrador del Puerto de Santa Fe (EAPSF). The project employed a strategic track, guided by four pillars, and a slope protection track, using a Multi-Criteria Decision Analysis (MCDA) to select a solution, resulting in a design containing both technical stability and a public urban concept.
The resulting urban concept, The Santa Fe Riverside Park, serves as a project embodying the strategic vision. The design integrates adaptive infrastructure, including stepped terraces and docking places, engineered to accommodate significant seasonal river fluctuations. This concept is supported by the delivery of a 15-year long-term roadmap. The unstable slope is protected using an ecosystem-friendly Articulated Concrete Block mattress system, improving the calculated sliding SF from 0.67 to 1.9, and achieving an erosion SF of 2.10.
Finally, the report provides the Port Authority with a strategic foundation of recommendations to realise the project.
...
The Port of Santa Fe was once a major hub for both domestic and international trade, but changing river dynamics have reduced its accessibility and economic importance. As a result, the port now faces the challenge of redefining its role and exploring new functions that reconnect the port with the public. The Dyke 2 waterfront in the Port of Santa Fe, is currently in a deteriorated and underdeveloped state, lacking essential public facilities, accessible green spaces, and safe access to the river. Most importantly, the site faces severe riverbank instability, confirmed by a calculated Safety Factor (SF) of 0.67.
This report presents an integrated vision and technical design for the sustainable redevelopment of the project site area, commissioned as an advisory document for the Ente Administrador del Puerto de Santa Fe (EAPSF). The project employed a strategic track, guided by four pillars, and a slope protection track, using a Multi-Criteria Decision Analysis (MCDA) to select a solution, resulting in a design containing both technical stability and a public urban concept.
The resulting urban concept, The Santa Fe Riverside Park, serves as a project embodying the strategic vision. The design integrates adaptive infrastructure, including stepped terraces and docking places, engineered to accommodate significant seasonal river fluctuations. This concept is supported by the delivery of a 15-year long-term roadmap. The unstable slope is protected using an ecosystem-friendly Articulated Concrete Block mattress system, improving the calculated sliding SF from 0.67 to 1.9, and achieving an erosion SF of 2.10.
Finally, the report provides the Port Authority with a strategic foundation of recommendations to realise the project.
This report presents an integrated vision and technical design for the sustainable redevelopment of the project site area, commissioned as an advisory document for the Ente Administrador del Puerto de Santa Fe (EAPSF). The project employed a strategic track, guided by four pillars, and a slope protection track, using a Multi-Criteria Decision Analysis (MCDA) to select a solution, resulting in a design containing both technical stability and a public urban concept.
The resulting urban concept, The Santa Fe Riverside Park, serves as a project embodying the strategic vision. The design integrates adaptive infrastructure, including stepped terraces and docking places, engineered to accommodate significant seasonal river fluctuations. This concept is supported by the delivery of a 15-year long-term roadmap. The unstable slope is protected using an ecosystem-friendly Articulated Concrete Block mattress system, improving the calculated sliding SF from 0.67 to 1.9, and achieving an erosion SF of 2.10.
Finally, the report provides the Port Authority with a strategic foundation of recommendations to realise the project.