Welcome to Virtual Fly Brain

A hub for Drosophila melanogaster neural anatomy and imaging data

You can explore via images/stacks of the central nervous system

or simply search for the item you're interested in using the search box in the menu bar:

Search by any neuropil, neuron, lineage clone, tract or specific image stack name

What can VFB do for me? Example queries with detailed steps

Anatomy information for the whole nervous system

For more information on this type of query go here.

  • Searches of this kind can be done straight from any page on the site, using the search bar on the header.
  • Use the search box on the header bar, and start typing saddle or any other synonym, such as SAD.
  • Choose the term saddle from the autocomplete list.
  • The page shows, on the left, the viewer, with the saddle highlighted, and on the right, the information for that term (term info window). The symbol next to the neuropil name indicates that that domain is displayed in the viewer.
  • Below the viewer is the viewer menu. Any entity that is displayed in the viewer is listed in the Displayed tab. You can centre, hide, delete or add that neuropil to the query builder using the buttons in the display column of the Displayed tab.
  • You can also interact with the viewer using the buttons on top of it. These include a slice browser, zoom, plane of view and changing background colour.
  • Further queries are now possible from the Query for menu, at the top of the term info window. Hover on the query options to the right of it to see all available queries. Choose the desired option and click to run the query.

For more information on this type of query go here.

  • Searches of this kind can be done straight from any page on the site, using the search bar on the header.
  • In the search box start typing antennal mechanosensory and motor centre or any synonym such as AMMC.
  • Choose the term from the autocomplete list. A page with all the information about that neuropil will be displayed.
  • The page shows, on the left, the viewer, with the saddle highlighted, and on the right, the information for that term (term info window). The symbol next to the neuropil name indicates that that domain is displayed in the viewer.
  • Below the viewer is the viewer menu. Any entity that is displayed in the viewer is listed in the Displayed tab. You can centre, hide, delete or add that neuropil to the query builder using the buttons in the display column of the Displayed tab.
  • The query menu, Query for, is shown at the top of the term info window. Click on the arrowheads to see all available sub-options.
  • Select the query Neurons with: synaptic terminals here.
  • A list with the query results will be displayed. Clicking on any of the names of the neuron types will display the viewer and term info window for that neuron type.
  • If images are available for a neuron type, they will be displayed in the 'Available Images' column. Click the Open button to display all neuron images of that type in the Viewer. Clicking on the List all button, will list all images for that neuron type. From there, you can add images to the Viewer one by one by clicking on the button.
  • If you want to find neurons that arborise in AMMC and in another neuropil, you can use one of our other tools, Query Builder. For more information on this type of query click here.

    • Query builder queries are made from the Viewer page. The query will be shown in the Query Builder tab.
    • To add a neuropil to the viewer, use the search box on the header, the Anatomy tab, or double-click on a neuropil directly in the viewer. Click on the symbol for the neuropil to be displayed in the viewer.
    • All images displayed in the viewer are listed in the Displayed tab.
    • To add a term to a Query Builder query, click the button. In the tab Query Builder, choose the type of terminals.
    • Add another neuropil in the same way. The query text below will be updated to reflect your query.
    • The number of records found is shown at each step.
    • When happy with your query, and the number of records is more than 0, click the Show Results button.

For more information on this type of query click here.

  • Searches of this kind can be done straight from any page on the site, using the search bar on the header.
  • In the search box, start typing antennal lobe or any known synonym, such as AL.
  • Choose the term from the autocomplete list, adult antennal lobe .
  • A page with all the information about that neuropil will be displayed.
  • The page shows, on the left, the viewer, with the saddle highlighted, and on the right, the information for that term (term info window). The symbol next to the neuropil name indicates that that domain is displayed in the viewer.
  • Below the viewer is the viewer menu. Any entity that is displayed in the viewer is listed in the Displayed tab. You can centre, hide, delete or add that neuropil to the query builder using the buttons in the display column of the Displayed tab.
  • Further query options are available from Query for. Click on the arrowheads to see all available sub-options.
  • Select the query: Lineage clones with: some part here.
  • A list with the query results will be displayed. If images are available, they will be shown in the Available Images column.
  • Click on More info or on the name of the clone to see more details about each lineage clone, including synonyms and thumbnail image. You can display the lineage clone images on the Stack Viewer by clicking the symbol. Either display all at once by clicking the latter, or list the images first, using List all and then choose which one to display. In this way you will be able to overlay any of the painted neuropil domains on the brain, together with the lineage clone.
  • To find neurons, or other clones that are part of this lineage select the query form the term info page for a clone, for example ALad1: Component of.
    Did you know? If you know which neuroblast lineage you are looking for, you can search directly for adult X lineage clone, where X is the neuroblast you want.
  • A list of neuron types and clones is displayed. To list all images for that neuron type, click on the List all button. You can now add them one by one to the viewer, by clicking the button. To display all at once use the Open button instead. To see all the information available for each neuron type, click on More info. Did you know? From this term info page, you can also directly query for transgenes expressed in that neuron class.
  • The list of all the neuron images is organised into 7 columns: ID, name of the neuron, definition, image thumbnail, source, neuron type and driver used.
  • To see a neuron in the Viewer, click on the symbol after its name.
  • You can add any other neuron or neuropil images to the viewer by clicking on the symbol. For example, click on the name of the image to see the term info window, and add a neuropil that is overlaps with, shown in the Relationships section.

Expression and images of single neurons, transgenes and lineage clones

For more information on this type of query click here.

  • Searches of this kind can be done straight from any page on the site, using the search bar on the header.
  • In the search box start typing ellipsoid body any known synonym, such as EB.
  • Choose the term, ellipsoid body from the autocomplete list.
  • A page with all the information about that neuropil (term info window) will be displayed.
  • The page shows, on the left, the viewer, with the saddle highlighted, and on the right, the information for that term (term info window). The symbol next to the neuropil name indicates that that domain is displayed in the viewer.
  • Below the viewer is the viewer menu. Any entity that is displayed in the viewer is listed in the Displayed tab. You can centre, hide, delete or add that neuropil to the query builder using the buttons in the display column of the Displayed tab.
  • Further query options are available from Query for. Click on the arrowheads to see all available sub-options.
  • Select the query Images of neurons with: some part here (clustered by shape).
  • A list with the query results will be displayed. These are organised by cluster of neurons (group of similar neurons) that overlap the ellipsoid body, and these are named by the exemplar of the cluster. A thumbnail image of the cluster exemplar is also shown. This allows you to quickly scan the clusters to find the neurons you are interested in.
  • The result list has six columns: on the left is a snapshot of the cluster, followed by the exemplar, summary, source, exemplar preview. The last column presents an option to display all images of the neurons in a specific cluster in the viewer, or to list them.
  • Clicking on the cluster snapshot will take you to the cluster page. There, you can see a 3D rendering of the cluster (in WebGL), and interact with it (rotate, zoom). In addition, the page displays a list of the neurons in that clusters sorted by similarity score, and a list of the top 5 clusters most similar to that one.
  • Back on the result list, clicking on List individual members, displays a list of all the neurons that are part of that cluster. The results are organised in seven columns: id, name of the neuron, definition, image thumbnail, source, neuron type and driver.
  • To open a neuron in the viewer, click on the next to the neuron name. To open all neurons in the results list, click the Open in viewer button, at the top of the table.
  • The number of stacks added to the viewer is shown on the green Stack Viewer button in the page header. Click on the button to go to the viewer.
  • In addition to images, you can also add neuropils to the viewer. Search from them using the search box in the page header.

For more information on this type of query click here.

  • Searches of this kind can be done straight from any page on the site, using the search bar on the header.
  • In the search box, start typing mushroom body alpha/beta neuron or any known synonym, such as alpha/beta Kenyon cell.
  • Choose the term from the autocomplete list.
  • A page with all the information about that neuron type (term info window) will be displayed.
  • The page shows, on the left, the viewer, with the saddle highlighted, and on the right, the information for that term (term info window). The symbol next to the neuropil name indicates that that domain is displayed in the viewer.
  • Below the viewer is the viewer menu. Any entity that is displayed in the viewer is listed in the Displayed tab. You can centre, hide, delete or add that neuropil to the query builder using the buttons in the display column of the Displayed tab.
  • The query menu, Query for, is shown at the top of the term info window. Hover to see all available sub-options.
  • Select the query Expression/Phenotypes found here: Transgenes expressed here.
  • A list with the query results will be displayed.
  • If images for the expression pattern of the driver are available they will be shown.
    Did you know? If you don't find all the results that you hoped, try running the same query for the neuropils, that is mushroom body alpha, mushroom body beta lobe, or adult mushroom body.

Generating a composite view

  • You can overlay as many images as you would like on the viewer. Click on the button that appears close to an image name, or if it is a group of neurons, on the Open button, and that image will be added to the viewer.
  • In the same way as with image stacks, neuropil domains can also be displayed in the viewer by clicking on the button.
  • Searches for images of neuron types, lineage clones or neuropils can be done straight from any page on the site, using the search bar on the header.
  • The number of stacks added to the viewer is shown on the green Stack Viewer button in the page header. Click on the button to go to the viewer.
  • The Displayed tab on the menu shows all images that are currently being displayed.
  • Each display is associated to a URL which you can share with others. In the Displayed tab, click on Copy URL to retrieve it.
  • You can save this URL anywhere in a text file or share it with others. Paste the URL in a browser address bar to view that specific combination of images.
  • To clear the viewer, use the Clear all button in the viewer menu, or the header menu 'Stacks > Clear items'.
  • Displayed entities are remembered between visits.

What's new

New NBLAST tool to find GAL4s that label specific neurons.

Revamped layout and viewer, cleaner and user-friendly

Tell us about your newly published paper

For full details about the site see the features page.

News

  • Major new VFB release
    New VFB release with lots of new data, inc 18K VT line images (BrainBase, VDRC) + 50% FlyCircuit neurons classified

  • Using NBLAST and VFB
    Find similar neurons and GAL4 drivers online

  • New site live
    Our new cleaner and slicker VFB 1.5 site is now live


More »





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