Talk:Human Embryo Collections

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Kyoto Collection

"Approximately 44,000 human embryos and fetuses have been collected and stored at Kyoto University over the past four decades, with the aid of several hundred obstetricians. In the majority of the cases, pregnancy was terminated for social reasons during the first trimester of pregnancy (the Maternity Protection Law of Japan) and healthy embryo generally were derived from the pregnancies. The pregnancies were mainly terminated by dilatation and curettage. Some specimens were derived from spontaneous or threatened abortions. Because the attending obstetricians did not examine the aborted materials, the collection of embryos was not biased by their outcome (normal or abnormal, live or dead, etc.) and the embryo collection can be considered to be representative of the total intrauterine population in Japan."

Imaging of a large collection of human embryo using a super-parallel MR microscope

Magn Reson Med Sci. 2007;6(3):139-46.

Matsuda Y, Ono S, Otake Y, Handa S, Kose K, Haishi T, Yamada S, Uwabe C, Shiota K. Source Institute of Applied Physics, University of Tsukuba, Ibaraki, Japan.

Abstract

Using 4 and 8-channel super-parallel magnetic resonance (MR) microscopes with a horizontal bore 2.34T superconducting magnet developed for 3-dimensional MR microscopy of the large Kyoto Collection of Human Embryos, we acquired T(1)-weighted 3D images of 1204 embryos at a spatial resolution of (40 microm)(3) to (150 microm)(3) in about 2 years. Similarity of image contrast between the T(1)-weighted images and stained anatomical sections indicated that T(1)-weighted 3D images could be used for an anatomical 3D image database for human embryology.

PMID 18037794

http://mrlab.frsc.tsukuba.ac.jp/human_embryos/

Graphic and movie illustrations of human prenatal development and their application to embryological education based on the human embryo specimens in the Kyoto collection

Dev Dyn. 2006 Feb;235(2):468-77.

Yamada S, Uwabe C, Nakatsu-Komatsu T, Minekura Y, Iwakura M, Motoki T, Nishimiya K, Iiyama M, Kakusho K, Minoh M, Mizuta S, Matsuda T, Matsuda Y, Haishi T, Kose K, Fujii S, Shiota K. Source Congenital Anomaly Research Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan.

Abstract

Morphogenesis in the developing embryo takes place in three dimensions, and in addition, the dimension of time is another important factor in development. Therefore, the presentation of sequential morphological changes occurring in the embryo (4D visualization) is essential for understanding the complex morphogenetic events and the underlying mechanisms. Until recently, 3D visualization of embryonic structures was possible only by reconstruction from serial histological sections, which was tedious and time-consuming. During the past two decades, 3D imaging techniques have made significant advances thanks to the progress in imaging and computer technologies, computer graphics, and other related techniques. Such novel tools have enabled precise visualization of the 3D topology of embryonic structures and to demonstrate spatiotemporal 4D sequences of organogenesis. Here, we describe a project in which staged human embryos are imaged by the magnetic resonance (MR) microscope, and 3D images of embryos and their organs at each developmental stage were reconstructed based on the MR data, with the aid of computer graphics techniques. On the basis of the 3D models of staged human embryos, we constructed a data set of 3D images of human embryos and made movies to illustrate the sequential process of human morphogenesis. Furthermore, a computer-based self-learning program of human embryology is being developed for educational purposes, using the photographs, histological sections, MR images, and 3D models of staged human embryos. Copyright 2005 Wiley-Liss, Inc.

PMID 16317724

http://onlinelibrary.wiley.com/doi/10.1002/dvdy.20647/full

http://onlinelibrary.wiley.com/store/10.1002/dvdy.20647/asset/supinfo/jws-dvdy.20647.anim2.mov?v=1&s=ef8bf74b5406772cc5949c94cb79e8918bc35fad

Normal and abnormal development of human embryos: first report of the analysis of 1,213 intact embryos

Teratology. 1968 Aug;1(3):281-90.

Nishimura H, Takano K, Tanimura T, Yasuda M. PMID 5759548

Carnegie Collection

The manifestation of the axes of the human embryo

Ronan O'Rahilly

http://www.springerlink.com/content/r0uw70l3m4651002/


Modeling Man: The Monkey Colony at the Carnegie Institution of Washington's Department of Embryology, 1925-1971

J Hist Biol. 2011 Apr 19.


Source National Museum of Health and Medicine, 6900 Georgia Ave, NW, Building 54, Washington, DC, 20307, USA, emily.k.wilson@gmail.com.

Abstract

Though better recognized for its immediate endeavors in human embryo research, the Carnegie Department of Embryology also employed a breeding colony of rhesus macaques for the purposes of studying human reproduction. This essay follows the course of the first enterprise in maintaining a primate colony for laboratory research and the overlapping scientific, social, and political circumstances that tolerated and cultivated the colony's continued operation from 1925 until 1971. Despite a new-found priority for reproductive sciences in the United States, by the early 1920s an unfertilized human ovum had not yet been seen and even the timing of ovulation remained unresolved. Progress would require an organized research approach that could extend beyond the limitations of working with scant and inherently restrictive human subjects or with common lab mammals like mice. In response, the Department of Embryology, under the Carnegie Institution of Washington (CIW), instituted a novel methodology using a particular primate species as a surrogate in studying normal human reproductive physiology. Over more than 40 years the monkey colony followed an unpremeditated trajectory that would contribute fundamentally to discoveries in human reproduction, early embryo development, reliable birth control methods, and to the establishment of the rhesus macaque as a common model organism.

PMID 21503772

Blechschmidt Collection

(University of Goettingen, Germany)

Managing Director Prof. Dr. J. Staiger Phone: 7052 Fax: 14016

Prof. Dr. Jochen Staiger, jochen.staiger@med.uni-goettingen.de

  • Professor E. Blechschmidt embryological collection were assigned Carnegie Nos. 10315-10434 in 1972.
  • because Professor Blechschmidt's wish was and is to have his collection combined with the Carnegie Collection.
  • Blechschmidt Collection was housed temporarily in the Department of Anatomy of Louisiana State University, New Orleans, under the care of Dr. Raymond F. Gasser.
  • basis of two important atlases (Blechschmidt, 1963, 1973)
    • Blechschmidt, E. 1963. Der menschliche Embryo. Dokumen- tationen zur kinetiscben Anatomie. Schattauer, Stuttgart.
    • Blechschmidt, E. 1973. Die prdnatalen Organsysteme des Menschen. Hippokrates, Stuttgart.
  • three-dimensional reconstructions are housed in the Anatomisches Institut der Universitat Gottingen.
  • the staging of these embryos has not been completed.


Ziegler Models

Book - Embryos in Wax: Models from the Ziegler Studio

http://www.vanleestantiques.com/subcat.php?id=86

Hubrecht Collection

A treasure house of comparative embryology

Int J Dev Biol. 1999;43(7):591-602.

Richardson MK, Narraway J. Source Department of Anatomy and Developmental Biology, St. George's Hospital Medical School, London, United Kingdom. m.richardson@sghms.ac.uk

Abstract

The Embryo Collection of the Hubrecht Laboratory is a treasure house of comparative embryology. It is the largest and most important collection of its kind in the world, and consists of thousands of vertebrate embryos stored in alcohol, or prepared as histological sections. Many elusive species are included in the collection, some represented by complete developmental series. The accompanying archives offer a remarkable insight into the methods used to collect embryos form wild animals, as well as the motives behind the founders of the collection. Carefully maintained, documented and catalogued, the collection is available for study by all interested scientists. We argue that this collection is one of the greatest biodiversity resources in existence.

PMID 10668968

http://www.intjdevbiol.com/paper.php?doi=10668968

A brief history of the Hubrecht Laboratory

Int J Dev Biol. 1999;43(7):583-90.

Faasse P, Faber J, Narraway J. Source Hubrecht Laboratory, Netherlands Institute for Developmental Biology, Utrecht.

PMID 10668967

http://www.intjdevbiol.com/paper.php?doi=10668967

Hill Collection

Duke University Comparative Embryology Collection

Harvard Collection

Harvard Collection

Paris Embryological Collection

An Acad Bras Cienc. 1990 Mar;62(1):79-84. Development of the coronary arteries in staged human embryos (the Paris Embryological Collection revisited). Mandarim-de-Lacerda CA. Author information

Abstract

Twenty seven human embryos from stages 15 to 23 (postsomitic period), belonging to the collection of the "UFR Biomédicale des Saints-Pères, Université René Descartes Paris V", were studied. Details of the aorticopulmonary cleavage were analysed specially aortic valve development and origin of the coronary artery. At stage 18 the aortic valve was clearly distinguished (cup-shaped) presenting semilunar valves and aortic sinus (Valsalvae); at this stage the left coronary artery was detected in 66.7 per cent of the cases as an endothelial epicardial invagination. At stage 19, the left and right coronary arteries were detected simultaneously in 100 per cent of the cases. At stage 20, the coronary arteries showed greater structural complexity with a coat of mesenchymal cells. These results agree with previous data from different embryological collections. These findings suggest that the left coronary artery has a tendency to develop earlier than the right. We found no evidence of the coronary origin from the aortic lumen. This work provides additional information about the embryological development of the heart, obtained from the analyses of a French collection of human embryos.

PMID 2097914

HuDSeN

Human Developmental Studies Network (HuDSeN)

http://www.hudsen.org

http://www.hudsen.eu

DOI: 10.1111/j.1469-7580.2010.01290.x

http://onlinelibrary.wiley.com/doi/10.1111/j.1469-7580.2010.01290.x/abstract;jsessionid=7D56A296108D4E410AB20D5F7C5624C1.f04t01

The corticofugal neuron-associated genes ROBO1, SRGAP1, and CTIP2 exhibit an anterior to posterior gradient of expression in early fetal human neocortex development

Cereb Cortex. 2011 Jun;21(6):1395-407. doi: 10.1093/cercor/bhq219. Epub 2010 Nov 8.

Ip BK1, Bayatti N, Howard NJ, Lindsay S, Clowry GJ. Author information

Abstract Developing neocortical progenitors express transcription factors in gradients that induce programs of region-specific gene expression. Our previous work identified anteriorly upregulated expression gradients of a number of corticofugal neuron-associated gene probe sets along the anterior-posterior axis of the human neocortex (8-12 postconceptional weeks [PCW]). Here, we demonstrate by real-time polymerase chain reaction, in situ hybridization and immunohistochemistry that 3 such genes, ROBO1, SRGAP1, and CTIP2 are highly expressed anteriorly between 8-12 PCW, in comparison with other genes (FEZF2, SOX5) expressed by Layer V, VI, and subplate neurons. All 3 were prominently expressed by early postmitotic neurons in the subventricular zone, intermediate zone, and cortical plate (CP) from 8 to 10 PCW. Between 12 and 15 PCW expression patterns for ER81 and SATB2 (Layer V), TBR1 (Layer V/VI) and NURR1 (Layer VI) revealed Layer V forming. By 15 PCW, ROBO1 and SRGAP1 expression was confined to Layer V, whereas CTIP2 was expressed throughout the CP anteriorly. We observed ROBO1 and SRGAP1 immunoreactivity in medullary corticospinal axons from 11 PCW onward. Thus, we propose that the coexpression of these 3 markers in the anterior neocortex may mark the early location of the human motor cortex, including its corticospinal projection neurons, allowing further study of their early differentiation.

PMID 21060114

The HUDSEN Atlas: a three-dimensional (3D) spatial framework for studying gene expression in the developing human brain

J Anat. 2010 Oct;217(4):289-99. doi: 10.1111/j.1469-7580.2010.01290.x.

Kerwin J1, Yang Y, Merchan P, Sarma S, Thompson J, Wang X, Sandoval J, Puelles L, Baldock R, Lindsay S.

Author information

Abstract

We are developing a three-dimensional (3D) atlas of the human embryonic brain using anatomical landmarks and gene expression data to define major subdivisions through 12 stages of development [Carnegie Stages (CS) 12-23; approximately 26-56 days post conception (dpc)]. Virtual 3D anatomical models are generated from intact specimens using optical projection tomography (OPT). Using MAPAINT software, selected gene expression data, gathered using standard methods of in situ hybridization and immunohistochemistry, are mapped to a representative 3D model for each chosen Carnegie stage. In these models, anatomical domains, defined on the basis of morphological landmarks and comparative knowledge of expression patterns in vertebrates, are linked to a developmental neuroanatomic ontology. Human gene expression patterns for genes with characteristic expression in different vertebrates (e.g. PAX6, GAD65 and OLIG2) are being used to confirm and/or refine the human anatomical domain boundaries. We have also developed interpolation software that digitally generates a full domain from partial data. Currently, the 3D models and a preliminary set of anatomical domains and ontology are available on the atlas pages along with gene expression data from approximately 100 genes in the HUDSEN Human Spatial Gene Expression Database (http://www.hudsen.org). The aim is that full 3D data will be generated from expression data used to define a more detailed set of anatomical domains linked to a more advanced anatomy ontology and all of these will be available online, contributing to the long-term goal of the atlas, which is to help maximize the effective use and dissemination of data wherever it is generated. © 2010 The Authors. Journal of Anatomy © 2010 Anatomical Society of Great Britain and Ireland.

PMID 20979583


Expression of PLA2G6 in human fetal development: Implications for infantile neuroaxonal dystrophy

Brain Res Bull. 2010 Nov 20;83(6):374-9. doi: 10.1016/j.brainresbull.2010.08.011. Epub 2010 Sep 9.

Polster B1, Crosier M, Lindsay S, Hayflick S.

Abstract

Mutations in PLA2G6, which encodes calcium-independent phospholipase A(2) group VIA (iPLA2-VIA), underlie the autosomal recessive disorder infantile neuroaxonal dystrophy (INAD). INAD typically presents in the first year of life, and leads to optic atrophy and psychomotor regression. We have examined PLA2G6 expression in early human embryonic development by in situ hybridization. At Carnegie Stage (CS) 19 (approximately 7 post-conception weeks [PCW]), strong expression is evident in the ventricular zone (VZ) of midbrain and forebrain suggestive of expression in neural stem and progenitor cells. At CS23 (8PCW) expression is also detectable in the VZ of the hindbrain and the subventricular zone (SVZ) of the developing neocortex, ganglionic eminences and diencephalon. By 9PCW strong expression in the post-mitotic cells of the cortical plate can be seen in the developing neocortex. In the eye, expression is seen in the lens and retina at all stages examined. PLA2G6 expression is also evident in the alar plate of the spinal cord, dorsal root ganglia, the retina and lens in the eye and several non-neuronal tissues, including developing bones, lung, kidney and gut. These findings suggest a role for PLA2G6 in neuronal proliferation throughout the developing brain and in maturing neurons in the cortical plate and hindbrain. Although widespread PLA2G6 expression is detected in neuronal tissues, the pattern shows dynamic changes with time and indicates that INAD pathogenesis may begin prior to birth. 2010 Elsevier Inc. All rights reserved.

PMID 20813170


3 dimensional modelling of early human brain development using optical projection tomography

BMC Neurosci. 2004 Aug 6;5:27.

Kerwin J1, Scott M, Sharpe J, Puelles L, Robson SC, Martínez-de-la-Torre M, Ferran JL, Feng G, Baldock R, Strachan T, Davidson D, Lindsay S.

Abstract

BACKGROUND: As development proceeds the human embryo attains an ever more complex three dimensional (3D) structure. Analyzing the gene expression patterns that underlie these changes and interpreting their significance depends on identifying the anatomical structures to which they map and following these patterns in developing 3D structures over time. The difficulty of this task greatly increases as more gene expression patterns are added, particularly in organs with complex 3D structures such as the brain. Optical Projection Tomography (OPT) is a new technology which has been developed for rapidly generating digital 3D models of intact specimens. We have assessed the resolution of unstained neuronal structures within a Carnegie Stage (CS)17 OPT model and tested its use as a framework onto which anatomical structures can be defined and gene expression data mapped. RESULTS: Resolution of the OPT models was assessed by comparison of digital sections with physical sections stained, either with haematoxylin and eosin (H&E) or by immunocytochemistry for GAP43 or PAX6, to identify specific anatomical features. Despite the 3D models being of unstained tissue, peripheral nervous system structures from the trigeminal ganglion (approximately 300 microm by approximately 150 microm) to the rootlets of cranial nerve XII (approximately 20 microm in diameter) were clearly identifiable, as were structures in the developing neural tube such as the zona limitans intrathalamica (core is approximately 30 microm thick). Fourteen anatomical domains have been identified and visualised within the CS17 model. Two 3D gene expression domains, known to be defined by Pax6 expression in the mouse, were clearly visible when PAX6 data from 2D sections were mapped to the CS17 model. The feasibility of applying the OPT technology to all stages from CS12 to CS23, which encompasses the major period of organogenesis for the human developing central nervous system, was successfully demonstrated. CONCLUSION: In the CS17 model considerable detail is visible within the developing nervous system at a minimum resolution of approximately 20 microm and 3D anatomical and gene expression domains can be defined and visualised successfully. The OPT models and accompanying technologies for manipulating them provide a powerful approach to visualising and analysing gene expression and morphology during early human brain development.

PMID 15298700

http://www.biomedcentral.com/1471-2202/5/27

Professor Susan Lindsay

http://www.ncl.ac.uk/ion/staff/profile/susan.lindsay


Multiple Collections

Towards a 3-Dimensional Atlas of the Developing Human Embryo: the Amsterdam Experience

Reprod Toxicol. 2012 May 25. [Epub ahead of print]

de Bakker BS, de Jong KH, Hagoort J, Oostra RJ, Moorman AF. Source Department of Anatomy, Embryology & Physiology, Academic Medical Center, Amsterdam, The Netherlands.

Abstract

Knowledge of complex morphogenetic processes that occur during embryonic development is essential for understanding anatomy and to get insight in the pathogenesis of congenital malformations. Understanding these processes can be facilitated by using a three-dimensional (3D) developmental series of human embryos, which we aim to create in this project. Digital images of serial sections of 34 human embryos of the Carnegie Collection between Carnegie stages 7 (15-17d) and 23 (56-60d) are used to create 3D reconstructions of different organ systems. The software package Amira is used to align the sections and to create the 3D reconstructions. In this midway evaluation we show the first results of the atlas, containing 34 embryos with more than 13.500 manually annotated sections. The 3D models can be interactively viewed within a 3D-pdf. This will be the first complete digital 3D human embryology atlas of this size, containing all developing organ systems. Copyright © 2012. Published by Elsevier Inc.

PMID 22640940

http://www.sciencedirect.com/science/article/pii/S089062381200202X?v=s5


Serial sections of 34 human embryos between Carnegie stages 7 (15-17 days) and 23 (56-60 days) were used to create 3D reconstructions of all the different organs and organ systems. Two specimens per Carnegie stage were incorporated in this atlas. Digital images of a first series of sections from embryos of the Carnegie Collection and one embryo from the Cambridge University, were kindly provided by the Computer Imaging Laboratory of the Louisiana State University in New Orleans [26] and a stage 20 (51-53 days) embryo of our own collection was captured at the Academic Medical Center in Amsterdam. Additional images of a second series of sections were captured at the Carnegie Collection at the Human Developmental Anatomy Center of the Walter Reed Army Medical Center in Washington D.C. and digital images of one stage 9 (19-20 days) embryo from the Boyd Collection were provided by the Department of Physiology, Development and Neuroscience at the University of Cambridge, United Kingdom. Additional information about the specimens can be found in Table 1.

  • Elizabeth Lockett of the Human Developmental Anatomy Center at the National Museum of Health and Medicine in Silver Spring, DC for our privilege to use the valuable material of the Carnegie Collection.
  • Professor Graham Burton for providing the digital images of a stage 9 embryo of the Boyd Collection.
  • Professor Robert J. Cork and Professor Raymond F. Gasser of the DREM project provide pictures of the first series of sections of human embryos of the Carnegie Collection.


Steding’s collection of human embryos

Centre of Anatomy, University of Goettingen, Germany

<pubmed>20149609</pubmed>


Virtual Microscopy

Open Access Software

Google Earth

Virtual microscopy with Google-Earth: a step in the way for compatibility http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849394

OpenLayers

  • OpenLayers makes it easy to put a dynamic map in any web page. It can display map tiles and markers loaded from any source. http://openlayers.org

Slice

Used on BEST network.

The Open Microscopy Environment

http://www.openmicroscopy.org/site

http://downloads.openmicroscopy.org/omero/5.0.0/

Virtual microscopy with Google-Earth: a step in the way for compatibility http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849394


NYU Virtual Microscope

The NYU Virtual Microscope uses the Google Maps API to display, annotate, and navigate scanned slides.


https://code.google.com/p/virtualmicroscope/

https://code.google.com/p/virtualmicroscope/wiki/SlideTiler


Openslide

Appears to have died.

http://openslide.org/other-projects


Commercial software

Leica (Aperio)

SOMS UNSW Aperio ScanScope XT Slide Scanner

Olympus

Zeiss

Other

  • PathScan Enabler IV https://www.emsdiasum.com/microscopy/products/digital/histology_scanner.aspx ($2,195.00)
    • 7200 dpi resolution, 3.5 microns per pixel
    • scanner scans an area of 1.42 x 0.85 inches (36.14 x 21.59 mm)
    • resulting in useable images up to 10,248 x 6,120 pixels, uninterpolated.
    • File size can be as large as 188 megabytes.
    • Produces image files which can be saved in a variety of formats including TIFF, PICT, BMP, GIF, etc. Compatible with PC Windows based computers.

JPG

  • restriction of jpg files to a maximum size of 65,000 pixels (216)