Clearity Care
The science behind Clearity Care.
The research behind Clearity Care
Years of research into the first weeks of life.
Clearity Care builds on the work of Dr Bernadette de Bakker, physician and embryologist at Amsterdam UMC, and her research group. Since 2012 they have studied how a human embryo develops and how imaging can show it in three dimensions: a 3D atlas of human development, a biobank that parents can donate to, and micro-CT scans that show an embryo in micrometre detail.
The research group in numbers
- scientific publications
- 107
- citations
- 1,699
- awards and prizes for the group since 2009
- 25
- research grants since 2015
- 33
Publications and citations: Amsterdam UMC research profile, October 2026. Awards and grants: the group's own list.
“We are among the pioneers who utilize micro-CT to study human tissue.”
Milestones
- 2012
Towards a 3D atlas of the human embryo
The group sets out how it will map human development in three dimensions.
Read - 2016
A 3D atlas of human development, in Science
An interactive atlas and database of the human embryo, published in one of the world's leading journals.
Read - 2017
The Dutch Fetal Biobank
Founded so that parents can donate fetal tissue to research.
Read - 2020
A 6 week embryo in micrometre detail
The first clear 3D image of an embryo at six weeks, made with micro-CT. Radiology named it the best image of the year.
Read - 2022
University of Amsterdam Alumni Award
First prize, for the Dutch Fetal Biobank.
Read - 2023
A standard for embryo and fetal biobanks
A framework for how human embryonic and fetal tissue is collected and stored, in Developmental Cell.
Read - 2024
How parents feel about donating tissue
A study of parents' acceptance of fetal tissue donation, in JAMA Network Open.
Read - 2026
Miscarriage tissue research: still in its infancy
A review of what research on miscarriage tissue can tell, and how much is still unknown.
Read
Awards and prizes
Recognition for the group's work, from imaging to the biobank.
- 2023Radiology, Best Cover of the Century, first prize
- 2023New Scientist Science Talent PrizeBernadette de Bakker
- 2022University of Amsterdam Alumni Award, first prize, for the Dutch Fetal Biobank
- 2021Radiology, Top Image award, first prize
- 2026Young Investigator Award, De Snoo-van 't Hoogerhuijs FoundationYousif Dawood
- 2025AUF Impact Award, for engaging society through human developmental researchPuck Mulder
- 2024ToScA UK and Europe, London: Best Lightning Talk AwardPuck Mulder
- 2024ToScA UK and Europe, London: Poster Competition, first placeWenjing Gou
- 2024ToScA UK and Europe, London: Travel AwardsPuck Mulder and Wenjing Gou
- 2023Noorderheideprijs, Stichting Elise Mathilde Fonds and Koninklijke Maatschappij voor Natuurkunde
- 2023ISFRI Patricia Flach honorary award for best presentationDaniël Docter
- 2023Dr. E. Slager Award for best presentation at the Doelen conference
- 2023AR&D Travel GrantMarieke Buijtendijk
- 2022ToScA Micro-CT Image Competition, first prize
- 2019AMC Best PhD Thesis Award, first prize
- 2019Amsterdam Science & Innovation Award, Life Sciences
- 2019Young Investigator Award, De Snoo-van 't Hoogerhuijs Foundation
- 2017Best Amsterdam Cardiovascular Sciences publication
- 2017AMC Graduate School PhD Publication Award 2016, first prize
- 2017AMC profile prize, 3D Embryo Atlas team
- 2014AAA travel award, Experimental Biology, San Diego
- 2013AAA Visiting Scholarship, National Museum of Health and Medicine, Silver Spring
- 2013Bolk Award, Dutch Anatomical Association, oral presentation
- 2013AAA travel award, Experimental Biology, Boston
- 2009Best Honours Student Presentation Award
All publications
Every publication the research group lists, newest first, each with a link to the article.
202610 publications
- Intestine organotypic culture recapitulates human embryonic villus morphogenesis at week 8Tissue Barriers
- The ecto-endodermal boundary in the oral and pharyngeal mucosa: implications for the etiology of HPV-induced tumorsLife
- In memoriam: Kees de Jong (1950-2026)Journal of Plastination
- Vascular Neuroembryology: The Genesis of the Intracranial Arterial System and the Circle of WillisLife
- The vascular-osteogenic interface in craniofacial development: a structured review of emerging associations in congenital malformationsDevelopmental Biology
- The Human Organ AtlasScience Advances
- Mapping the prenatal growth of the mandibleJournal of Craniofacial Surgery
- Multi-omics investigation of thyroid development and dysfunction in down syndromeHuman Molecular Genetics
- Timing of Secondary Palate Fusion in Human Embryos and FetusesBirth Defects Research
- Miscarriage Tissue Research: Still in Its InfancyLife
202515 publications
- Should future cavum septi pellucidi be assessed during first‐trimester fetal brain examination?Ultrasound in Obstetrics & Gynecology
- The 4D Human Embryonic Brain Atlas: Spatiotemporal atlas generation for rapid anatomical changesComputerized Medical Imaging and Graphics
- Conversion to publication rate of Abstracts presented at Annual Congresses of the International Society of Forensic Radiology and imagingForensic Imaging
- Revealing the unseen: 3D synchrotron X-Ray imaging of uterine vasculature in adenomyosisAngiogenesis
- ISFRI Education Working Group: competencies and training requirements for reporting and interpretation of adult forensic post-mortem imagingForensic Imaging
- Robust Alignment of the Human Embryo in 3D Ultrasound Using PCA and an Ensemble of Heuristic, Atlas-Based and Learning-Based Classifiers Evaluated on the Rotterdam Periconceptional CohortLecture Notes in Computer Science
- Evaluating micro-computed tomography for investigation of the pediatric hyoid-larynx complexPediatric Radiology
- Micro-computed tomography to visualize preserved vascular architecture in decellularized human vaginal tissue: explorative studyScientific Reports
- An overview and evaluation of first-trimester physiological fetal human anatomy using 3-dimensional ultrasound combined with virtual reality techniquesHuman Reproduction
- The cochlear basal turn as a very preserved region in cochlear hypoplasias: radiological and embryological considerations from a cohort of 125 patientsNeuroradiology
- The value of Micro-CT imaging in the forensic evaluation of neck traumaForensic Science International
- White paper by the international society of forensic imaging guidelines working group on non-contrast PMCT for SCUBA-related fatalitiesForensic Imaging
- ISFRI guidelines working group: Best practice standards for non-contrast postmortem computed tomography (PMCT) of overdoseForensic Imaging
- Microscopic and molecular analysis of the Urethral Plate: A Step Towards Improved Hypospadias Surgery OutcomesUrology
- Advancing understanding of anorectal malformations through micro-CT imaging of resected materialGastro Hep Advances
202411 publications
- Semi-supervised Three-Dimensional Detection of Congenital Brain Anomalies in First Trimester UltrasoundLecture Notes in Computer Science
- Imaging the development of the human craniofacial arterial system: an experimental studyPediatric Radiology
- Parental Acceptance of Fetal Tissue DonationJAMA Network Open
- Mineralization and thickness of the condylar cortex in skeletal remains of children’s mandibles: A preliminary studyArchives of Oral Biology
- Psychological sequelae following second‐trimester termination of pregnancy: A longitudinal studyActa Obstetricia et Gynecologica Scandinavica
- Pro-inflammatory T cells-derived cytokines enhance the maturation of the human fetal intestinal epithelial barrier. iScienceiScience
- High resolution imaging of human development: shedding light on contrast agentsNeuroradiology
- An open-source, three-dimensional growth model of the mandibleComputers in Biology and Medicine
- Diagnostic accuracy of ultrasound screening for fetal structural anomalies during the first and second trimester of pregnancy in low-risk and unselected populationsCochrane Database of Systematic Reviews
- Scaling Up Contrast-Enhanced Micro-Ct Imaging: Optimizing Contrast and Acquisition for Large Ex-Vivo Human SamplesForensic Imaging
- Micro‐ CT Imaging of Tracheal Development in Down Syndrome and Non‐Down Syndrome FetusesThe Laryngoscope
20237 publications
- Human embryonic and foetal biobanking: A framework for standardisation of proceduresDevelopmental Cell
- Away from definition and back to the clinic: As response to Kumar et al, ‘Evidence is not sufficient to declare the tubal gland conglomerates as salivary’Radiotherapy and Oncology
- Immunohistological profiling confirms salivary gland-like nature of the tubarial glands and suggests closest resemblance to the palatal salivary glandsRadiotherapy and Oncology
- Embryonic morphological development is delayed in pregnancies ending in a spontaneous miscarriageHuman Reproduction
- Discrepancies in Embryonic Staging: Towards a Gold StandardLife
- Morphological variations of the human spleen: no evidence for a multifocal or lobulated developmental originThe British Journal of Radiology
- Decrease in Prevalence of Cleft lip, Alveolus and Palate After Nationwide Introduction of the Second-Trimester Anomaly Scan in the NetherlandsThe Cleft Palate Craniofacial Journal
20227 publications
- Imaging fetal anatomySeminars in Cell & Developmental Biology
- Microfocus computed tomography for fetal postmortem imaging: an overviewPediatric Radiology
- Reconsidering the “non-recanalization theory” of the gutJournal of Developmental Origins of Health and Disease
- The developmental impacts of natural selection on human pelvic morphologyScience Advances
- A three‐dimensional analysis of the development of cranial nerves in human embryosClinical Anatomy
- Impact of surgery and anesthesia during early brain development: A perfect stormPediatric Anesthesia
- Comparison of postmortem whole‐body contrast‐enhanced microfocus computed tomography and high‐field magnetic resonance imaging of human fetusesUltrasound in Obstetrics & Gynecology
20219 publications
- The important role of RPS14, RPL5 and MDM2 in TP53-associated ribosome stress in mycophenolic acid-induced microtiaInternational Journal of Pediatric Otorhinolaryngology
- The Legend of the Buffalo ChestChest
- Reducing soft-tissue shrinkage artefacts caused by staining with Lugol's solutionScientific Reports
- Increased nuchal translucency before 11 weeks of gestation: Reason for referral?Prenatal Diagnosis
- Synchronized broadcast spawning by six invertebrates (Echinodermata and Mollusca) in the north-western Red SeaMarine Biology
- Where do sperm and egg meet?Reproduction
- Initial morphological symmetry breaking in the foregut and development of the omental bursa in human embryosJournal of Anatomy
- The tubarial salivary glands: A potential new organ at risk for radiotherapyRadiotherapy and Oncology
- Development pattern of tracheal cartilage in human embryosClinical Anatomy
202022 publications
- The Developmental Origin of the Auricula RevisitedThe Laryngoscope
- The tubarial glands paper: A starting point. A reply to comments in 8 letters to the editorRadiotherapy and Oncology
- Incidence of Symptomatic Submucous Cleft Palate in the Netherlands: A Retrospective Cohort Study Over a Period of 22 YearsThe Cleft Palate Craniofacial Journal
- Three-dimensional visualizations from a dataset of immunohistochemical stained serial sections of human brain tissue containing tuberculosis related granulomasData in Brief
- Mitchell-Riley syndrome iPSC exhibit reduced pancreatic endoderm differentiation due to an RFX6 mutationDevelopment
- Fecal microbiota transplantation halts progression of human new-onset type 1 diabetes in a randomized controlled trialGut
- The immunological architecture of granulomatous inflammation in central nervous system tuberculosisTuberculosis
- Micro-CT of Early Human DevelopmentRadiology
- Massive gas embolisms in diving fatalities visualized by radiology and neuropathologyClinical Neuropathology
- Symbiotische samenwerking tussen patholoog en radioloogMemorad
- Prevalentie van bullae en blebs bij post-mortem CT. Implicaties voor duikgeneeskunde?Memorad
- Postmortale beeldvorming van foetussenMemorad
- Endoscopic Cauterization and Sclerotherapy for Airway Obstruction by a Third Branchial Pouch SinusThe Laryngoscope
- Engineering Heart MorphogenesisTrends in Biotechnology
- Fracture patterns of the hyoid-larynx complex after fatal trauma on the neck: retrospective radiological postmortem analysis of 284 casesInternational Journal of Legal Medicine
- The most accurate postmortem radiological imaging method to evaluate suspected neck violenceForensic Imaging
- The brachial plexus: explaining its morphology and variability by a generic developmental modelJournal of Anatomy
- Reply to ‘Risk of barotrauma when diving with pulmonary bullae’Chest
- Prevalence of pulmonary bullae and blebs in post-mortem computed tomography with potential implications for diving medicineChest
- Novel imaging techniques to study postmortem human fetal anatomy: a systematic review on microfocus-CT and ultra-high-field MRIEuropean Radiology
- Development of the human heartAmerican Journal of Medical Genetics Part C: Seminars in Medical Genetics
- The impact of using three-dimensional digital models of human embryos in the biomedical curriculumAnnals of Anatomy: Anatomischer Anzeiger
20194 publications
- Variants of the hyoid-larynx complex, with implications for forensic science and consequence for the diagnosis of Eagle’s syndromeScientific Reports
- The Pronephros; a Fresh PerspectiveIntegrative and Comparative Biology
- Conventional X-ray as an additional tool in the analysis of fatal neck traumaForensic Science, Medicine and Pathology
- The value of post-mortem computed tomography of burned victims in a forensic settingEuropean Radiology
20185 publications
- The development of the human notochordPLOS ONE
- The development of the human hyoid-larynx complex revisitedThe Laryngoscope
- On the Enigma of the Human Neurenteric CanalCells Tissues Organs
- Hitherto unknown detailed muscle anatomy in an 8‐week‐old embryoJournal of Anatomy
- Postmortem radiological case series of acetabular fractures after fatal aviation accidentsForensic Science, Medicine and Pathology
20174 publications
- Single‐site neural tube closure in human embryos revisitedClinical Anatomy
- The first-trimester fetal central nervous system: a novel ultrasonographic perspectiveAmerican Journal of Obstetrics and Gynecology
- Forensic radiology in the Netherlands: A personal perspectiveJournal of Forensic Radiology and Imaging
- The vanishing duodenal polyp: mesenteric invagination presenting as duodenal pseudopolypBMJ Case Reports
20162 publications
20151 publication
- Enkele anatomische structuren in menselijke vingergewrichten die een rol zouden kunnen spelen bij de pathogenese van reumatoïde artritisNederlands Tijdschrift voor Reumatologie
20141 publication
- Building foundations for transcatheter intervascular anastomoses: 3D anatomy of the great vessels in large experimental animalsInteractive CardioVascular and Thoracic Surgery
20132 publications
- Systematic analysis of the development of the ductus venosus in wild type mouse and human embryosEarly Human Development
- The use of 3D-CT in weapon caused impression fractures of the skull, from a forensic radiological point of viewJournal of Forensic Radiology and Imaging
20121 publication
- Towards a 3-dimensional atlas of the developing human embryo: The Amsterdam experienceReproductive Toxicology
PhD theses5
- Bridging the gap in orofacial cleft care: diagnosis, education and treatmentJ.A. Smit, 2026
- SEEING The Unseen: the importance of prenatal screeningM.A. Lugthart, 2024
- Anomalies of the larynx and trachea: developmental aspects and treatment considerationsM.M. Fockens, 2024
- Forensic Radiology in the Netherlands: results of a symbiotic collaboration in the pathological-radiological fieldH.M. de Bakker, 2020
- 3D Atlas of Human Embryology: new insights in human developmentB.S. de Bakker, 2018
Book chapters6
- Post Mortem Imaging of the Fetus & Child: A Comprehensive Guide (chapter)Springer Nature, ed. Owen Arthurs, 2024
- Novel 3D imaging techniques in early pregnancyEarly Pregnancy, 3rd edition, Cambridge University Press, ed. Marjet Goddijn, 2024
- Embryonic & fetal growth and developmentTextbook of obstetrics and gynaecology, 2nd edition, Bohn Stafleu van Loghum, 2024
- Anatomy of the female pelvis, pelvic organs & reproductive systemTextbook of obstetrics and gynaecology, 2nd edition, Bohn Stafleu van Loghum, 2024
- Embryonic & fetal growth and developmentTextbook of obstetrics and gynaecology, Bohn Stafleu van Loghum, 2019
- Anatomy of the female pelvis, pelvic organs & reproductive systemTextbook of obstetrics and gynaecology, Bohn Stafleu van Loghum, 2019