David H Hall et al. (2002) West Coast Worm Meeting "Wormatlas: A web-based behavioral and structural atlas of C. elegans"

Thomas Boulin, Zeynep F Altun, Michael Zhang, Maurice Volaski, Constantinos Polydorou, David H Hall

[West Coast Worm Meeting, 2002]

We have recently launched the prototype of Wormatlas (www.wormatlas.org). This atlas is designed to serve the scientific community with the main goal of bringing all the anatomical information pertinent to C. elegans within one readily accessible and easy to use web site. By creating extensive links to the WormBase as well as the C. elegans WWW server, we are aiming to provide users with seamless links between these databases. We hope to create the most comprehensive and complete online anatomy atlas for any genetic model organism.

David H Hall et al. (2002) East Coast Worm Meeting "Wormatlas: A web-based behavioral and structural atlas of C. elegans"

David H Hall, Maurice Volaski, Michael Zhang, Constantinos Polydorou, Thomas Boulin, Zeynep F Altun

[East Coast Worm Meeting, 2002]

We have recently launched the prototype of Wormatlas (www.wormatlas.org). This atlas is designed to serve the scientific community with the main goal of bringing all the anatomical information pertinent to C. elegans within one readily accessible and easy to use web site. By creating extensive links to the WormBase as well as the C. elegansWWW server, we are aiming to provide users with seamless links between these databases. We hope to create the most comprehensive and complete online anatomy atlas for any genetic model organism. Wormatlas is designed to have two main sections, Index and Guides, with multiple chapters within each section. The Index section will contain the Handbook, Slidable Worm, Literature Archive, Cell Identifications, Neuron Data, Glossary, and Methods. The main goal of the Handbook is to provide a relatively simplified, image-supported and curated information about the general and specific anatomy of C. elegans.The images included in the Handbook will be annotated scanning and transmission electron (TEM) micrographs, computer-drawn images as well as DIC and fluorescent micrographs. The Slidable Worm is designed to provide 600-1200 annotated and nonannotated versions of TEM cross-sections of the animal available for viewing by the users with the help of a newly designed JAVA applet interface. The images will come from the original images from the MRC/LMB archive, from the MIT archive (courtesy of E. Hartwieg and R. H. Horvitz), from our Caltech/AECOM archives, and possibly others. The Literature Archive will provide on-line copies of landmark articles and treatises about the anatomy of the nematode. These HTML format articles include multiple web links to other sites in Wormatlas and WormBase to strengthen their interactivity for the structures mentioned. The Glossary aims to provide a comprehensive list of all nomenclature used to describe any cell structure in the nematode. Cell Identification and Neuron Data are planned to provide enough detail on features of single cells, esp. neurons, to aid researchers in recognizing and studying individual cells by their 3D shapes and positions, comparing TEM, DIC and GFP information, and by providing links to curated data on their gene expression patterns. Finally, Anatomical Methods will provide an up to date summary of the different modalities that are currently used in cell identification and tissue pathology studies. This website is designed to accommodate the vast amount of structural, behavioral and gene expression data that has appeared since publication of The Mind of a Worm in a dynamic and easily updatable medium. This curated information can be viewed in individual neuron pages as well as neuron data appendices. In the future, we want to develop interactive user interfaces to visualize behavioral circuitries and perhaps neurophysiology information as they become available. The second section of Wormatlas provides guides for optimal usage of the information included in the first section. It offers general information relevant to C. elegans as well as specific usage directions for Wormatlas. For instance, we have created a color coding system in which the main structural elements of the animal have each been assigned a specific color from the web-safe color palette. The uniform color code will help viewers to perceive anatomical relationships and tissue symmetries even without any symbolic annotation. Our close collaboration with WormBase researchers has helped to create a common display language, in data sharing, and in development of a shared Gene Ontology vocabulary. Wormatlas is being created to serve the scientific community and as such, we greatly appreciate your input, data sharing, suggestions and criticisms that help improve the web site. We are actively seeking peer review as each new chapter is readied for release.

David H Hall et al. (2002) Mid-west Worm Meeting "Wormatlas: A web-based behavioral and structural atlas of C. elegans"

David H Hall, Zeynep F Altun, Constantinos Polydorou, Thomas Boulin, Maurice Volaski, Michael Zhang

[Mid-west Worm Meeting, 2002]

We have recently launched the prototype of Wormatlas (www.wormatlas.org). This atlas is designed to serve the scientific community with the main goal of bringing all the anatomical information pertinent to C. elegans within one readily accessible and easy to use web site. By creating extensive links to the WormBase as well as the C. elegansWWW server, we are aiming to provide users with seamless links between these databases. We hope to create the most comprehensive and complete online anatomy atlas for any genetic model organism. Wormatlas is designed to have two main sections, Index and Guides, with multiple chapters within each section. The Index section will contain the Handbook, Slidable Worm, Literature Archive, Cell Identifications, Neuron Data, Glossary, and Methods. The main goal of the Handbook is to provide a relatively simplified, image-supported and curated information about the general and specific anatomy of C. elegans.The images included in the Handbook will be annotated scanning and transmission electron (TEM) micrographs, computer-drawn images as well as DIC and fluorescent micrographs. The Slidable Worm is designed to provide 600-1200 annotated and nonannotated versions of TEM cross-sections of the animal available for viewing by the users with the help of a newly designed JAVA applet interface. The images will come from the original images from the MRC/LMB archive, from the MIT archive (courtesy of E. Hartwieg and R. H. Horvitz), from our Caltech/AECOM archives, and possibly others. The Literature Archive will provide on-line copies of landmark articles and treatises about the anatomy of the nematode. These HTML format articles include multiple web links to other sites in Wormatlas and WormBase to strengthen their interactivity for the structures mentioned. The Glossary aims to provide a comprehensive list of all nomenclature used to describe any cell structure in the nematode. Cell Identification and Neuron Data are planned to provide enough detail on features of single cells, esp. neurons, to aid researchers in recognizing and studying individual cells by their 3D shapes and positions, comparing TEM, DIC and GFP information, and by providing links to curated data on their gene expression patterns. Finally, Anatomical Methods will provide an up to date summary of the different modalities that are currently used in cell identification and tissue pathology studies. This website is designed to accommodate the vast amount of structural, behavioral and gene expression data that has appeared since publication of The Mind of a Worm in a dynamic and easily updatable medium. This curated information can be viewed in individual neuron pages as well as neuron data appendices. In the future, we want to develop interactive user interfaces to visualize behavioral circuitries and perhaps neurophysiology information as they become available.

Robyn Lints et al. (2004) East Coast Worm Meeting "Frogs and snails and puppy dog tails? Wormatlas launches a guide to what boy worms are made of."

Robyn Lints, Zeynep F Altun, Huawei Weng, David H Hall, Maurice Volaski, Gloria Stephney

[East Coast Worm Meeting, 2004]

C. elegans is sexually dimorphic, producing hermaphrodite and male sexes that differ from one another in both their morphology and behavior. The hermaphrodite has been studied extensively and over the past three years we have developed a web-based guide to its anatomy (www.wormatlas.org) designed to assist researchers with interests ranging from gene characterization to computational modeling. In addition, The Handbook, Glossary and selected Slideable Worm electron micrographs (EMs) from the site are to be published as a laboratory handbook in the coming year (Cold Spring Harbor Laboratory Press, NY). As part of our long-term objective to describe C. elegans developmental stages and sexes, we are now embarking on a description of the male anatomy. Males differ from hermaphrodites primarily in the reproductive tract and in the tail, which bears the male copulatory apparatus (1, 2). The male has a single-armed gonad containing a germ line that produces only sperm. The tract opens to the exterior at the male anus (cloaca) via a modified rectal epithelial chamber called the proctodeum. The tail copulatory apparatus is organized around this opening and consists of the copulatory spicules, several types of male-specific external sensory organs, interneurons, motor neurons and muscles. Most male-specific cells arise post-embryonically through sex-specific division of precursors common to both sexes. Thus, establishing the adult male form involves the generation and organization of a large number of male-specific cells and their integration into an existing framework of non-sex-specific tissues. Several studies have assigned roles for male-specific cells in fascinating sex-specific behaviors such as mate-searching (3) and copulation (4). However, a full understanding of these behaviors requires a detailed knowledge of the cellular substrates underlying their expression, both at the level of individual cells and the functional units they form through their interconnection. In contrast to the hermaphrodite, the male anatomy is only partially described and, in particular, the connectivity of many male neurons is still unknown. To resolve this problem, we are currently collaborating with the Emmons lab to describe the fine structure and connectivity of individual neurons and other cell types in the male. This project resumes the effort initiated by the MRC in the 1970s to reconstruct the male posterior nervous system from the N2Y EM series. Emerging connectivity data will be incorporated into a web-based guide to the male anatomy. The male anatomy will be presented in a format similar to that used for the hermaphrodite. Additional features we hope to incorporate in the future include a Slideable Male Worm, 3D models of cell shapes generated from EM serial reconstructions and quick-time movies of those important events in a male's life. We anticipate that the male web pages will provide a comparative basis for gene expression or developmental studies and represent a significant advancement on current descriptions of this sex. It is our hope that, through this multi-tiered web-based description and an accompanying handbook, the workings of at least this male sex will become less of a mystery. 1. Horvitz and Sulston (1977) Dev. Biol. 56, 110-156. 2. Sulston et al. (1980) Dev. Biol. 78, 542-576. 3. Lipton and Emmons (2003) J. Neurobiol 54: 93-110. 4. Sternberg and Emmons (1997). In C. elegans II (Eds. Riddle et al., CSHL Press, NY), pp. 295-334.

Robyn Lints et al. (2004) West Coast Worm Meeting "Frogs and snails and puppy dog tails? Wormatlas launches a guide to what boy worms are made of."

Zeynep F Altun, Huawei Weng, Maurice Volaski, Gloria Stephney, Robyn Lints, David H Hall

[West Coast Worm Meeting, 2004]

C. elegans is sexually dimorphic, producing hermaphrodite and male sexes that differ from one another in both their morphology and behavior. The hermaphrodite has been studied extensively and over the past three years we have developed a web-based guide to its anatomy (www.wormatlas.org) designed to assist researchers with interests ranging from gene characterization to computational modeling. In addition, The Handbook, Glossary and selected Slideable Worm electron micrographs (EMs) from the site are to be published as a laboratory handbook in the coming year (with Cold Spring Harbor Laboratory Press, NY). As part of our long-term objective to describe C. elegans developmental stages and sexes, we are now embarking on a description of the male anatomy. Males differ from hermaphrodites primarily in the reproductive tract and in the tail, which bears the male copulatory apparatus (1, 2). The male has a single-armed gonad containing a germ line that produces only sperm. The tract opens to the exterior at the male anus (cloaca) via a modified rectal epithelial chamber called the proctodeum. The tail copulatory apparatus is organized around this opening and consists of the copulatory spicules, several types of male-specific external sensory organs, interneurons, motor neurons and muscles. Most male-specific cells arise post-embryonically through sex-specific division of precursors common to both sexes. Thus, establishing the adult male form involves the generation and organization of a large number of male-specific cells and their integration into an existing framework of non-sex-specific tissues. Several studies have assigned roles for male-specific cells in such fascinating sex-specific behaviors as mate-searching (3) and copulation (4). However, a full understanding of these behaviors requires a detailed knowledge of the cellular substrates underlying their expression, both at the level of individual cells and the functional units they form through their interconnection. In contrast to the hermaphrodite, the male anatomy is only partially described and, in particular, the connectivity of many male neurons is still unknown. To resolve this problem, we are currently collaborating with the Emmons lab to describe the fine structure and connectivity of individual neurons and other cell types in the male. This project resumes the effort initiated by the MRC in the 1970s to reconstruct the male posterior nervous system from the N2Y EM series. Emerging connectivity data will be incorporated into a web-based guide to the male anatomy. The male anatomy will be presented in a format similar to that used for the hermaphrodite. Additional features we hope to incorporate in the future include a Slideable Male Worm, 3D models of cell shapes generated from EM serial reconstructions and quick-time movies of those important events in a male's life. We anticipate that the male web pages will provide a comparative basis for gene expression or developmental studies and represent a significant advancement on current descriptions of this sex. It is our hope that, through this multi-tiered web-based description and an accompanying handbook, the workings of at least this male sex will become less of a mystery. 1. Horvitz and Sulston (1977) Dev. Biol. 56, 110-156. 2. Sulston et al. (1980) Dev. Biol. 78, 542-576. 3. Lipton and Emmons (2003) J. Neurobiol 54: 93-110. 4. Sternberg and Emmons (1997) In C. elegans II (Eds. Riddle et al., CSHL Press, NY), pp. 295-334.

Robyn Lints et al. (2005) International Worm Meeting "WormAtlas Update"

Zeynep F Altun, Gloria Stephney, David H Hall, Huawei Weng, Robyn Lints, Maurice Volaski, Tylon Stephney

[International Worm Meeting, 2005]

WormAtlas (www.wormatlas.org) is a web site for C. elegans anatomy that uses illustrations, various modes of microscopy and computer models to describe the animals anatomy. As part of our long-term goal to describe C. elegans developmental stages and sexes, we are nearing the completion of the adult hermaphrodite handbook. Recently posted is an informative description of the animals muscle system including a 3D model based on serial section electron micrograph (EM) data that shows the physical relationship between muscle arms and motor neurons. During 2004 we began a handbook dedicated to the male starting with an overview of sexually dimorphic tissues and guides to gender identification. More recent additions include a description of the male musculature containing substantial unpublished data from MRC archives. Working closely with the Male Wiring Project (see Xu et al., this meeting) we have also been posting new male connectivity data as it emerges. Even at this early stage of its description, it is evident that male cell biology differs in a number of ways: some tail neurons are much more branched than is typically observed in C. elegans, many sensory neurons are also motor neurons, and muscles are not necessarily innervated via arms. Our most recent and exciting development is the launch of The Worm Image Database (see Weng et al., this meeting). This database will provide the community with online access to more than 200,000 EM images in our archives, generated by the community over the past 30 years and now housed at the Center for C. elegans Anatomy. This collection includes the MRC series used to reconstruct the hermaphrodite nervous system and the N2Y series currently being used by the Male Wiring Project to reconstruct the male connectivity. This searchable database will later be extended to include light microscopy images. Archival descriptors such as source, stage, gender and preparation method will automatically be retrieved with the images. In future, users will be able to add annotations to the descriptors that may be shared privately among a work group, or publicly with the community at large. The database will not only give users ready access to irreplaceable community resources, but also provide a powerful mechanism for knowledge and data sharing. Our thanks to community members who have generously shared data with our Center.

Tylon Stephney et al. (2007) International Worm Meeting "WormImage: An online photo album for C. elegans electron microscopy."

Huawei Weng, Maurice Volaski, David H. Hall, Toni Long, Kevin Fisher, Meng Xu, Tylon Stephney

[International Worm Meeting, 2007]

The Hall lab is the home for the physical EM data for C. elegans that was collected by many scientists working at several key laboratories over the past 40 years. We have almost all of the annotated prints, negatives, data notebooks and often the original thin sections and blocks from the MRC, Missouri, Caltech and AECOM collections, including the work of John White, John Sulston, Sam Ward, and many others. This archive includes wild type and mutant data, and covers both males and hermaphrodites, and all ages from embryo to adulthood, and some aging animals. We are scanning much of this physical print data to produce a digital archive of C. elegans anatomy. We have generated about 3 terabytes of digital images, and there is much more scanning to be done. We have designed a simple online photo album, WormImage, to share some of this archive as small thumbnail versions that can quickly transit across the Internet to all users, for free. Bandwidth issues limit our ability to ship full size scans electronically, but we also supply users with higher resolution scans upon request, by ftp or on DVDs. WormImage (www.wormimage.org) is an online database developed for remote retrieval of this digitized microscopy data. Currently this database contains about 20,000 different digital images. Most scans have been taken from the workprints, to preserve original hand annotations which mark identified cell types. The WormImage database is updated weekly to provide more images. The user can search this database by animal name, age, sex, or by regional information (head, midbody, tail) or by tissue types to identify potential images of interest. The user can quickly survey many animals in small thumbnail images, or concentrate on details of a few images expanded to larger size. The program was recently revised to make it easy for the user to click through all the thumbnails for one animal in serial order. Hall has been reviewing the original annotations and writing brief summaries for each animal, also offered on the website. These Color Code summaries help to translate the shorthand markings on the original prints into the familiar cell names for many structures. During 2007, WormImage will begin showing images of key mutant phenotypes and aging animals. We are grateful to Demian Nave and Art Wetzel at the Pittsburgh Supercomputing Center for their help in providing a mirror site. This work is funded by NIH RR 12596.