About the project

The idea of this project was born in 2012 when the Laboratory of Evolutionary Morphology of the Zoological Institute RAS (Saint Petersburg) had received for safekeeping a neurohistological collection of G.A. Nevmyvaka, an outstanding, but undeservedly forgotten neuromorphologist, a disciple of A.A. Zavarzin and a proponent of his ideas on the nervous system of invertebrates. The collection was donated by the relatives of G.A. Nevmyvaka, who kept it for many years at home. As it turned out, the collection included not only the preparations made by G.A. Nevmyvaka, but also some neurohistological preparations made by A.A. Zavarzin, which were superbly preserved despite being about one hundred years old. The majority of preparations were stained supravitally by methylene blue. This staining method was developed at the end of the 19th century by A.S. Dogiel at the Saint-Petersburg University and can be justifiably regarded as a uniquely informative and still relevant technique for studying the nervous system (for more detail, see Neurohistology methods). Unfortunately, in all textbooks and academic papers on the invertebrate nervous system, the images made using this staining method were represented only by hand-drawn pictures of whole-mount preparations. Due to a number of mostly technical reasons, no photographs have ever been made from these preparations. With the burgeoning of immunohistochemical methods and the advent of confocal microscopy, this technique and the possibilities for its application have undeservedly been consigned to obscurity.

For many years, our laboratory was a center for studying the evolutionary morphology of the invertebrate nervous system and has amassed a large collection of neurohistological preparations of representatives of various animal groups. In 2015–2016, we have received several large collections of preparations made by eminent invertebrate neurohistologists, Yu.P. Lagutenko and S.I. Plotnikova. On S.I. Plotnikova’s request, we have also taken for safekeeping all preparations of A.A. Zavarzin (her stepfather) that she had been keeping.

As an homage to the Russian neurohistological school and its founders, we have decided not only to preserve and when necessary to restore the neurohistological collections that we have at our disposal, but also, whenever possible, to provide them with annotations and make at least some of them available to the public. This prompted the idea of creating a publicly accessible and educational database in the form of the Atlas of morphology of the animal nervous system.

The creation of systematized thematic databases is an efficient solution for the digitization, systematization and combining the existing and constantly updating data in different areas of biology, ecology and medicine. The nervous system is one of the major functional systems of any multicellular animal. It is the primary integrative system of any organism, which gives it the ability to perceive the surrounding world and to shape its behavior by responding to the external cues. Our knowledge of the architecture of the nervous system is pivotal for all kinds of neurobiological research: from studying individual neurons to analyzing complex behavioral reactions and mechanisms of memory. The morphology of the nervous system is characterized both by a high degree of evolutionary conservation and a high evolutionary plasticity and, for this reason, is also used as a reliable source of taxonomic characters. Our Atlas can, therefore, be of interest to a wide range of specialists and to all who are curious about the biodiversity of the animal world and wants to unravel the mysteries of the nervous system.

There are currently no categorized and systematized databases on the nervous system of both invertebrate and vertebrate animals. Moreover, the atlases on the nervous system of invertebrate animals are also almost entirely lacking. This is primarily explained by a vast diversity of the morphologies of the nervous system in invertebrates and the paucity of information compared to the nervous system of vertebrates and also by a narrow specialization of many scientists who focus their research on a limited range of animals and methods. On the other hand, the zoological collections are usually not created with the intention to preserve the morphological material as permanent histological preparations and/or electron databases of their photographs. These highly valuable sources of information are not documented as annotated collections, and therefore are not available to the public. Unfortunately, research institutions and zoological museums often pay little attention to the conservation and safekeeping of histological preparations, even though these preparations are especially valuable for our understanding of the animal morphology and its diversity and can become an important part of the preserved collections. To overcome these difficulties, an additional work is need, which involves registering the histological preparations or images made from these preparations as inventory items, i.e. making a detailed description of each item (study object, visualization method, annotation of the structures visible in the images, etc.), so that the preparation can be understood not only by specialists, but also by a wider public.

Making histological preparations, especially those intended for studying the nervous system, is a complex and laborious work. This work requires not only the skills and experience gained over many years of practice, but also an individual approach and sometimes specifically developed methods for studying new regions of the nervous system or new animal species. The possibility of getting new knowledge on the organisation of the nervous system is directly dependent on the effectiveness of the methods used and on the quality of preparations. For this reason, the personality of a scientist plays a crucial role in these studies and the successful preparations made by the scientist are essentially unique and require not only special care in their handling, but also a detailed accompanying description.

All of these considerations have laid the groundwork for our project. The realization of the project became possible on the server of the Zoological Institute RAS with the financial support from the Russian Foundation for Basic Research (grant No. 15-29-02650). The project also greatly benefited from the assistance of our colleagues from the Koltsov Institute of Developmental Biology RAS (IDB RAS, Moscow) and the Department of Cytology and Histology of the Saint-Petersburg State University and their collections of histological preparations that show the development of the nervous system in invertebrates and the morphology of the vertebrate telencephalon. Our Atlas also incorporated a large collection of instructional preparations of the nervous system, sensory structures and the embryonic nervous system of higher vertebrates and humans, which is stored at the Department of Histology and Embryology of the Knorre Saint-Petersburg State Pediatric Medical University (SPSPMU). Somewhat later, the project was joined by the researchers from the Sechenov Institute of Evolutionary Physiology and Biochemistry who had previously worked with S.I. Plotnikova and are the specialists in the insect nervous system.

Our aim for the Atlas was not only to preserve the existing collections and make their inventory by converting them into digital images, but also to arrange the atlas in such a way as to allow the users to develop a deeper understanding of the diversity, evolutionary patterns and developmental processes of the brain and sensory systems. Unlike other similar databases, our database was specifically designed as a compendium of high-quality images that illustrate the hypotheses describing the evolutionary patterns and developmental processes and show the diversity and harmony of the nervous system. The atlas is based on the images taken from the preparations of 30 collections, whose major part is stored at the Laboratory of Evolutionary Morphology of the Zoological Institute RAS (Saint Petersburg). Some collections are stored at the Department of Cytology and Histology of the Saint-Petersburg State University, at the IDB RAS, IEPB RAS and SPSPMU. Collections include permanent and virtual preparations (i.e. series of photographs taken from temporary preparations using confocal microscopy) that illustrate the evolution and development of the nervous system in Acoela, Plathelminthes, Rotifera, Nemertini, Mollusca, Annelida, Bryozoa, Echinodermata, Insecta, and Craniata. Many of these collections are constantly being expanded by new preparations.

The work on the project began with the development of the database schema that was suitable for the comprehensive description of the images. Data representation was standardized for all images, which allowed for a flexible data input where the preparation can be represented not only by a single image, but also by a whole series of optical sections made at different depths in the preparation, and in some cases by complete 3D reconstructions. It should be noted that the database was structured in such a way as to allow for its further expansion and development.

The next important phase of the project was the development of the website structure, which was to become the foundation for the arrangement and indexing of the texts that accompany and supplement the illustrations. The Atlas is subdivided into several sections that allow for the maximum use of all available illustrative resources of the database for different purposes and to answer different questions that could be asked by the users: to learn about the nervous system of a particular animal group; to find information about the methods used in studying the nervous system and their benefits and disadvantages; to learn which species are used as animal models in neurobiological studies or in developing the methods for biotesting and bioindication; and to learn about the patterns of evolution and development of the nervous system.

The next important phase of the project was the development of the website structure, which was to become the foundation for the arrangement and indexing of the texts that accompany and supplement the illustrations. The Atlas is subdivided into several sections that allow for the maximum use of all available illustrative resources of the database for different purposes and to answer different questions that could be asked by the users: to learn about the nervous system of a particular animal group; to find information about the methods used in studying the nervous system and their benefits and disadvantages; to learn which species are used as animal models in neurobiological studies or in developing the methods for biotesting and bioindication; and to learn about the patterns of evolution and development of the nervous system.

The third phase of the project, which is still ongoing, is the constant updating of the database with new texts and images. The work on the project proved to be more difficult than was thought in the beginning. The greatest amount of effort and time was expended on the sorting and arrangement of old collections made by the scientists that had passed away. Most of their preparations lacked any clear accompanying labels. To restore the missing information, the preparations were carefully examined by a specialist who knew well the general organization of the nervous system in this animal group and the methods used to make the preparation, and was familiar with the scientific works, which contained the drawings of the preparations made by the author of the collection. Each collection was provided with a detailed description and with the biography and major publications of its author. Much of this information, especially concerning the authors of the previous century, has never before been published on the web or was previously only partially available.

A lot of time was spent to select the preparations from each collection, which could serve as the best representations of the structure of the nervous system and of the methods used. The magnification and the region of the preparation, from which the photographs were made, were also carefully selected. A significant work was done to annotate the images and enter their full description into the database.

Each of the main participants took part in writing the texts for those sections of the Atlas, which matched their area of expertise. These sections were supplemented by references to publications.

1. Olga V. Zaitseva (doctor of biological sciences, chief staff scientist, Head of the Laboratory of Evolutionary Morphology, Zoological Institute RAS) is the author of the project’s general concept; she participated in designing the database and developing the structure of the website, took part in sorting and describing the collections and in making the annotations for the preparations selected for the Atlas; provided images for the website, wrote texts for several webpages including the biographies of the authors, and edited all texts for the website.
2. Mikhail B. Dianov (Head of the IT group (computer center) of the Zoological Institute RAS, system administrator) compiled and maintained the database, participated in coding the dynamic webpages for the site and provided the technical assistance for the project.
3. Anatoly A. Petrov (candidate of biological sciences, senior staff scientist of the Laboratory of Evolutionary Morphology, Zoological Institute RAS) designed and created all static webpages for the site, participated in designing the database and describing the collections, made some images for the site and participated in making the annotations; wrote texts for several webpages of the site and translated most of the text into English.
4. Aleksandr N. Shumeev (candidate of biological sciences, staff scientist of the Laboratory of Evolutionary Morphology, Zoological Institute RAS) participated in designing the database and photographed most of the preparations selected for the Atlas, made most of the work for the annotations of preparations and took major part in editing the data for the database.
5. Elena E. Voronezhskaya (doctor of biological sciences, chief staff scientist of the Institute of Developmental Biology RAS, Head of the Laboratory of Comparative Developmental Physiology, Project Supervisor for the RFBR grant that funded the works on the Atlas) wrote texts for several webpages of the site, provided some images and participated in making the annotations.
6. Dmitriy K. Obukhov (doctor of biological sciences, professor of the Department of Cytology and Histology of the Saint-Petersburg State University) wrote texts for several webpages of the site, provided some images and participated in making the annotations.
7. Victor V. Starunov (candidate of biological sciences, staff scientist of the Laboratory of Evolutonary Morphology, Zoological Institute RAS) participated in designing the database and in sorting the collections, photographed and annotated the preparations selected for the Atlas, wrote texts for several webpages of the site and translated them into English.
8. Roman V. Smirnov (candidate of biological sciences, staff scientist of the Laboratory of Evolutionary Morphology, Zoological Institute RAS) wrote texts for several webpages of the Atlas and translated them into English, participated in sorting the collections and preparations, photographed preparations for the Atlas and participated in creating the annotations and entering data into the database.
9. Elena A. Kotikova (doctor of biological sciences, leading staff scientist of the Laboratory of Evolutionary Morphology, Zoological Institute RAS) wrote texts for several webpages of the Atlas, provided images for these webpages and for the database, and participated in making annotations for the Atlas.
10. Sergey A. Petrov (junior staff scientist of the Laboratory of Evolutionary Morphology, Zoological Institute RAS) participated in making photographs for the collections, preparing the annotations and entering data into the database.
11. Kseniya V. Shunkina (candidate of biological sciences, staff scientist of the Laboratory of Evolutionary Morphology, Zoological Institute RAS) wrote texts for several webpages of the Atlas, translated them into English, and provided some images and annotations for the database.
12. Tatyana V. Kuznetsova (candidate of biological sciences, senior staff scientist of the Saint-Petersburg Research Center for Environmental Safety RAS) arranged and annotated her collection, and participated in annotating the collection of A.A. Zavarzin and selecting preparations for photographs.

The other participants involved in the project are Olga I. Raikova (candidate of biological sciences, senior staff scientist of the Laboratory of Evolutionary Morphology, Zoological Institute RAS), Irina Yu. Severina (senior staff scientist of the Institute of Evolutionary Physiology and Biochemistry RAS), Inga L. Isavnina (junior staff scientist of the Institute of Evolutionary Physiology and Biochemistry RAS), Elizaveta G. Fofanova and Aleksandra L. Obukhova (junior staff scientists of the Laboratory of Comparative Developmental Physiology, Institute of Developmental Biology RAS). These participants created the annotations and provided images for their collections.

Although the works on the project are still underway, the Atlas is now available for use. In addition to completing the work on the already-planned sections of the Atlas, we also plan to continue updating the database with new images from the collections that we currently have and bring into the project new specialists and their images of the nervous system. We also intend to create new sections for the Atlas, for instance, those devoted to the pathologies of the nervous system or to other groups of animals. We wish for our website to become a guidebook for the nervous system of animals and an interactive encyclopedia on its morphology, evolution and development, the study methods and the use of animal models in neurobiology, developmental biology and biotechnology. We hope that other researchers studying the nervous system will take interest in our ideas and will join our project. We are open for cooperation and hope to find people who share our ideas. You can send your suggestions or proposals (in Russian or English) to this email address: neuromorphology@zin.ru.