Microbial Life > Topics of Interest > Special Collections > micro*scope

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 microorganisms—both 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
micro*scope asset page
A typical micro*scope asset page.

Inside micro*scope


  1. 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.
  2. Collections: When possible, each image is placed into a collection of similar images. For example, the Microbes of Mono Lake collection includes about 50 images of various types of microbes found in Mono Lake, CA. Collections are especially helpful as a reference for environmental observations. A person looking at ponds in Wyoming, for instance, may find it helpful to refer to the Freshwater Ponds of Idaho collection when identifying unknown organisms.
  3. 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 taxa—usually 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.
  4. 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.
  5. 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.
  6. 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.
  7. Glossary: A dynamic, image-rich glossary of protistology, microscopy, and general microbiology terms is accessible via the left-hand navigation menu.

micro*scope Structure


micro*scope structure
micro*scope heirarchical structure

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.

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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.

  • Browse Organisms Alphabetically
    Browse Organisms link in micro*scope

    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
    Browse Classification menu in micro*scope

    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
    Browse Recent Addition menu in micro*scope

    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
    Browse Collection menu in micro*scope

    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
    Browse Concept menu in micro*scope

    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.

  • Search the Site
    Search micro*Scope 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
    Search micro*scope 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
    Search micro*scope 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.

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micro*scope Terminology


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