Archives
The archival collection is stored in shelved cupboards (Fig. 1A), in locked rooms with a controlled access. The slides, on which series of adjacent sections through human embryos or fetuses are mounted, are slotted vertically into compartmentalized and labelled wooden boxes (Fig. 1 B, C). The slides are placed in an educational context within the relevant institutions of Anatomy.
Shelved cupboards in which the boxes of slides are stored.
Examples of the wooden boxes in which the slides are stored, each of a capacity of 200. Each box bears a label detailing pertinent information appertaining to the preparations.
The inset of a wooden box within which the slides are slotted vertically.
Methods
The slides were scanned over a period of 2 years by a group of biomedical and medical students. For this purpose, a Hamamtsu Nanozoomer (S60) was employed, a special adjustment of which was required by one of the firm’s technicians to accommodate the large glass slides (52 mm x 76 mm).
The sections were stained according to standard protocols, the most used agent being Haematoxylin and Eosin (HE), He-Orange, Azan and Nissl. The original images can be viewed with the readily available NDP.view2 software of Hamamatsu.
The slides were first cleaned with ethanol, and sometimes, the coverslip had to be removed to eliminate air bubbles (Fig. 2A, B). The slips were then remounted or, if necessary, replaced by the technician (Mrs. Marlène Sanchez, University of Fribourg) (Fig. 2C).
Air bubbles trapped beneath the coverslip.
Air bubbles disappear upon mounting the new coverslip.
Coverslip removed and replaced with a larger one to embrace formerly exposed edges of the tissue.
The large slides were lotted into custom-made metal holders (Fig. 3A), which were inserted into a Nanozoomer rack (Fig. 3B). Using a 40x-objective, up to 30 slides could be sequentially scanned in a batch mode (Fig. 3C). The scanned areas were 4’000 mm2 and the scanning time approximately 30 minutes per slide. Between 12 and 15 hours were required to scan an entire batch of slides.
Metal holder prepared in the workshop of the Physics Department of the University of Fribourg.
Rack with a metal holder containing a slide.
Hamamatsu holder, wit 3 x 10 slides ready to be scanned.
The quality of the images was then evaluated, blurred ones being eliminated and repeated. The pictures of good quality were stored (130 TB) on a university server, under the control of a computer scientist (Felix Meyenhofer, University of Fribourg).
Fifty-six-superbly prepared- sequential transverse sections through Embryo E44 (CRL: 8,5 mm), mounted on a single glass slide (52 x 76 mm).
The identity number of the Embryo (or Fetus) from which the sections originated was written on each slide and on the cover of the wooden box from which they were derived. A flashcard was prepared for each embryo, bearing information appertaining to the CRL-length, the thickness of the section, the fixation technique, the staining protocol, and the number of sections prepared.
In rare instances, the boxes held drawings and handwritten notes, some examples of which are given below (Fig. 5).
Drawing and remarks concerning sections through the hand and clavicula of E1203.
Flashcard with a telegraphic summary of the most important information appertaining to the sections through E597, E895 and E879, including their location within the boxes.
Photograph of Embryo E98 (CRL: 10.5 mm). Transverse sections mounted on 49 glass slides. Size of the scan: 420 GB.
Telegraphic report of the technician, pasted on the lid of the wooden box. Slide 27 is noted as missing.
Photograph of Embryo E6 (CRL: 7mm); transverse sections mounted on 9 slides. Total size of scan: 83.5 GB.
Drawing of Embyo E5 (CRL: 4 mm); sagittal section mounted on 5 glass slides (slide number 2 was too thick to be scanned). Remnants of brown glue are visible. Total size of the scan 20.3 GB.
Acknowledgments
Dr. Dominique Loffing and Prof. Johannes Loffing (Zürich) strongly supported this project from the beginning and took care of regularly providing the sections for their transfer for scanning in Fribourg.
Felix Meyenhofer, our microscopist, and computer scientist (Bioimage Core Facility) established the image acquisition and data management workflow an contributed his technical support and expertise throughout this project. The historical embryo section collection required numerous customisations on the imaging equipment to deal with the non-standard object carriers (glass slides) and as well as challenges dealing with the large data volumes.
Helmut Teichmann of Hamamatsu Switzerland and his team of engineers (Julien Siue, Paris) were extremely helpful and allowed for an efficient and successful collaboration.
For more than three years (2018-2021), Fribourg students of biomedicine and medicine scanned slides of sections through human embryos of various stages of development with the Nanozoomer (Hamamatsu). Cand. Med. Emilie and Julien Hirt have distinguished themselves. The students received a modest salary, and the costs were assumed partly by the department of medicine (Prof. S. Cook), by the anatomy unit (Prof. L. Filgueira), as well by Swant Inc. and Frimorfo Inc..
Our IT specialist Eric Bourquard has conceived and prepared the web version of this Embryonic atlas and has uploaded it as a third part of the existing “www.embryology.ch” web site.