Initial Publication Date: October 11, 2006

**micro*scope**

micro*scope, http://microscope.mbl.edu, is a communal website that promotes information on the biodiversity of microbes. It includes images, descriptions and taxonomic classifications of microorganismsâboth prokaryotic and eukaryotic. The content of the website is freely available for educational use. It currently features almost 11,000 images!

Content - Structure - Find Information - Terminology

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**Inside micro*scope**

Images: micro*scope currently contains almost 11,000 images of microbes - prokaryotic and eukaryotic. All images are freely available for educational use.
- A download button on each organism (asset) page allows you to access larger files of the image (e.g. TIFF, PDF) for use in presentations and reports.
Collections: When possible, each image is placed into a collection of similar images.
Descriptions: All organism (asset) pages in micro*scope are accompanied with two types of descriptions. The description to the right of the image is a general description of the taxaâusually at the genus level. The description below the image is specific to only that image. It includes information about the organism, as well as where it can be found, what type of microscopy was used, name of the individual that contributed the image, and more.
Classification: Below the image on the left-hand side is a link to the underlying CU*STAR database. Clicking on the link will pull up the taxonomic classification for this particular organism.
Link*outs: These links appear on the right-hand side of the page and direct users to other informational pages about this organism. Clicking on the Ward's link, for example, will direct you to educational resources offered by Ward's Natural Science. The NCBI link will direct you to taxa-specific molecular data, PubMed will pull up related literature, and so on.
Screensavers: There are currently 4 sets of microbial screensavers available. They may be downloaded from the micro*scope home page under News.
- various microbes from the Microbial Life digital library
- marine microbes brought to you by the International Census of Marine Microbes
- microbes from extreme habitats brought to you by the NASA Astrobiology Institute
- microbial imagery from the Bay Paul Center.
Glossary: A dynamic, image-rich glossary of protistology, microscopy, and general microbiology terms is accessible via the left-hand navigation menu.

**micro*scope Structure**

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micro*scope has a hierarchical structure. There are databases that contain images, names, classifications, and descriptions of organisms. These pieces of information are joined together to form web pages about the organisms. One type of page emphasizes an image with a caption, organism name, name of parent collection, a description of the organism, link*outs, downloadable images, a button that will allow you to make comments. A second type of page emphasizes the classification. The contents are grouped together in collections - each usually coming from a different contributor. Collections are then organized by concept. This structure allows visitors to find information either by typing a name into a search box, or by browsing by concept (or alphabetically or by the classification scheme). Browsing allows you to make increasingly refined choices about which assets you want to see. The site is also assembling an illustrated glossary which can be accessed through the search button in the left hand menu bar.

**Finding Information in micro*scope**

There are many ways to find information in micro*scope. If you know what you want, use the search functions - either on the home page or in the left-hand menu bar. Browse allows you to navigate progressively towards information of interest. You may browse organisms alphabetically by genus name, by taxonomic classification, and/or by recent additions to the website. You can also browse through the collections using an alphabetical listing or by concept.

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Browse Organisms Alphabetically

This feature allows you to browse micro*scope by genus name. Begin on the home page of micro*scope. Use the left-hand navigation column to select browse / organisms / alphabetically. The alphabet and page numbers across the top will guide you through the entire collection of representative genera. You will find that there is a lot to chose from. Select an image to view all pages within a particular genus.
Browse Organisms by Classification

This feature allows visitors to browse organisms by hierarchical taxonomic classification. Begin on the home page of micro*scope. Use the left-hand navigation column to select organisms / by classification. In the classification box, select either viruses or cellular life. A drop-down list will appear. Select desired group and a second drop-down list will appear. You may continue to browse through the classification structure until you find the group/organism of interest. The classification we use is called CU*STAR and is a system that is still under development.

Note: We don't have pictures for all organisms in the classification structure. If micro*scope contains an asset page for the selected group/organism, images will appear on the right-hand side of the page. Click on an image to access its associated asset page. If descriptions are available, they will appear in the middle of the classification page above the link*outs. In those cases where we don't have images, you can always use the linkouts to find information at other web sites.
Browse Organisms by Recent Additions

This feature allows you to view the latest images added to the micro*scope database. Begin on the home page of micro*scope. Use the left-hand navigation column to select organisms / recent additions. A page of recent additions will appear. Select an image to view detailed information.
Browse Collections Alphabetically

This feature allows visitors to browse collections alphabetically. Begin on the home page of micro*scope. Use the left hand navigation column to select browse / collections / alphabetically. The alphabet across the top will guide you through all of the collections. Select a collection name to access related asset pages.
Browse Collections by Concept

This feature allows visitors to browse collections by concept, or theme. For example, concepts include freshwater, marine, sediment, extreme, and so on. Begin on the home page of micro*scope. Use the left hand navigation column to select in browse / collections / by concept. A brief list of concepts will appear on the left-hand side of the page, including geography and habitat. Select a category. A new page will appear listing all concepts within the chosen category. Select a concept to view a list of collections. Click a collection name to access asset pages housed in that collection.

Search micro*scope by using the search button on the top of the page or by the left-hand navigation bar. You may search for the names of organisms within the micro*scope website and its underlying classification structure, or search for keywords in the glossary.

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Search the Site

This feature allows visitors to search the entire micro*scope site by taxon or keyword. Begin on the home page of micro*scope. Use the left-hand navigation column to select search / this site. A search box will appear at the top of the page. Simply type in the name you want to find and select the search button. Results will appear in three categories: the CU*STAR database, formal descriptions, and image captions. Select a name from the CU*STAR database to access the taxonomic classification for the organism/group or select a name listed under descriptions or image captions to view the asset page featuring the search term.
Search Glossary

This feature allows you to search for terms in the glossary. Begin on the home page of micro*scope. Use the left-hand navigation column to select search / glossary. A search box will appear along with an alphabetical browse menu. Either click on a letter to browse the glossary or enter a keyword in the search box to locate a specific term. There is often a picture with each term - and if you need to know about a term that isn't in here, send an email to the site administrator (microscope@mbl.edu) and they'll try to add the term to the glossary for you.
Search Classification

This feature allows visitors to search the underlying classification index CU*STAR for any taxon. Begin on the home page of micro*scope. Use the left-hand navigation column to select search / classification. A search box will appear at the top of the page. Simply type in the name you want to find and select the Search button. When the results appear in the new window, select the name you want and click the Jump button. A hierarchical classification structure will appear below.

**micro*scope Terminology**

Assets are pieces of information to be included (in databases) within micro*scope. Currently, most assets are images but micro*scope is set up to allow for considerable flexibility as to the kinds of assets that may be included in the future. Assets are usually placed in collections.
Asset pages contain information and tools about individual taxa. Each asset page contains the asset (usually an image), name of organism, name of parent collection, general description, caption, link*outs, downloadable image button, links to a classification page, comments, PDF button, and additional assets.
Classification - within the context of the micro*scope, classification refers to the hierarchical classification of organisms - a biological classification.
Concept hierarchy is a hierarchical arrangement of assets. This is useful in allowing visitors to find assets by providing a limited number of opportunities to navigate through the hierarchy and make increasingly refined choices about which assets they wish to see. Concept hierarchy is an alternative means of finding assets to 'search' and is appropriate to visitors who have an imprecise idea of what they are looking for. It is created through the hierarchical arrangement of collections, and within micro*scope this is flexible and open-ended.
Collections are hierarchical organizations of assets within micro*scope. Assets (such as images) are placed inside collections (such as 'Flagellates of Botany Bay'). Collections may be placed within other collections to create one or more hierarchical organizations of assets.
Content Certified Link*outs offer taxon-specific links to external databases and web sites. The link*outs are selected by experts and so provide a means of accessing information that has been peer-reviewed. Content-certified linkouts will only be visible if there is information at the remote sites. Link*outs are mapped to the underlying CU*STAR classification system so that visitors are guided to other sites that may have content on the same organisms, and are not directed to sites that are not taxonomically relevant. Use link*outs to access external publications, cultures, images, and much more.
Contributors are those contributing assets to micro*scope or names and taxonomic expertise to the CU*STAR classification structure.
Database - a repository of electronic information. Data is located within tables, and tables are comprised of records, and records may contain one to many fields. In micro*scope, the databases are built in mySQL software. A table might, for example, contain information on images, and a particular record relating to a picture of a rock in the Eastern Sierras might have fields with the name of the image, the person who took the picture, the location of the image, and a description.
Descriptions are located on asset pages and on the CU*STAR classification page. They offer characteristics of the taxon, in general, and are not specific to a particular asset. Descriptions are drawn from a database called Bio*pedia.
Downloadable Images, if present, will cause a zipped tif version of the image to download to your site. The images (sometimes you will get more than you expect) that are downloaded are usually much larger than those on the web siteâfew are under 2MB. These images are suitable for uses other than display on a computer monitor; you may use them as presentations, posters, student documents, etc. The tif format for the images has been selected for images because it is not a lossy format, but you will probably find it easier to manipulate large files if you convert the image to a jpg imageâfor which you will need to use a graphics program such as Photoshop. If it is not feasible, a right mouse click on the image on this site will open up a menu which will allow you to download the image which you can see on the screen. This is a 72dpi jpg image, and is suitable for display on a computer monitor. Downloadable files are freely available for educational purposes. Commercial users should contact us.
Images are generally 400 x 350 pixels, 72 dpi, jpgs. Information regarding the type of microscopy used to obtain the image can be found in the last sentence of the image caption. Images are available in high-resolution and may be downloaded for free use by educators, students, and other non-commercial users. Commercial users need to make contact with the site manager - microscope@mbl.edu
Image Captions are long descriptions written by the contributor of the image. Information is specific to the image and includes a description, location of where the sample was collected, type of microscopy used, and individual(s)/institution to be credited.
Link*outs initiate taxon-specific searches into external databases and web sites. Link*outs are selected by experts and so provide a means of accessing information that has been peer-reviewed. Link*outs are mapped to the underlying CU*STAR classification system so that visitors are guided to other sites that may have content on the same organisms, and are not directed to sites that are not taxonomically relevant. Use link*outs to access external publications, cultures, images, and much more.
Taxa (plural taxon) refers to taxonomic groups or entities - one taxon, many taxa.
Visitor - a person visiting the micro*scope web site