MBAT User Workflows View an Atlas Open Data Upload Data Run a Query –Search Data Further Examination Microarray Data Further Examination of 2D Data –Search by ROI (?) Create an Atlas (not sure this would be here)

View an Atlas –User selects File: Open Atlas toolbar to open an atlas (MDA2006_STX.atlas is default for most of our functions). Associated image and label files are opened in the main window Associated.ilf file is opened, but the hierarchy is only seen if the user opens BrainGraph –For advanced users, they can open the following tools in the Tools menu to explore the atlas: BrainGraph-automatically loads the hierarchy specified by the current.ilf file (recommend this be default-which view would be default is TBD) 3D Viewer and Surface manager (may need to leave out of this version depending on time it takes to put it in new format) –The user must load the associated.3D atlas file (in the same folder) –Then the user must select which surfaces they wish to view

View Data –By default there are no open atlases –User selects File: Open –Then selects their file type to open data All images opened in this manner are opened in the main window Opening multiple datasets in the same window may cause problems with viewing unless they have the same dimensions-give a warning if the images are of different dimensions Some of these images will be easier to visualize using the Maximum Intensity tool (which gives a 2D image of a 3D volume)

Upload Data Currently the user accesses this directly in the Microarray Query panel Planned: The user will connect to a “workspace” or a simple interface to lead them to the appropriate upload interface. They are stepped through the full upload process once they reach the appropriate upload interface, –Current and most future upload interfaces will be web-based –This interface may be the BIRN data repository Upload interface, but it may not be ready in time For this Fall we will connect to two upload interfaces: –BIRN Microarray Upload Interface (for sure-potentially put in a MBAT window?) –UCSD 2D image Spatial Registration (behind the portal) (waiting on) 2D Spatial Registration need an Intermediate (allows us to grow easily)

Search Data Opening an Atlas is not required, but preferred –If they open the default atlas Microarray data will automatically be shown in the Atlas –If no atlas is opened, they will only view returned data-may be better for 3D volumes Launch Concept Query Tool Generate Query Review Results panel for data of interest Identify the results of interest to the User –Microarray data: sent to Microarray Data Explorer for further examination –2D images: sent to zViewer for further examination –3D volumes (if any): can be downloaded to computer and opened in MBAT main window, rather than download, potentially save in temp file and immediately open in MBAT window (?), sort of depends on how results come back download

Further Exploration of Microarray Data After Concept-based query sends Microarray data to the Data Explorer User has the ability to gather more information about the datasets in this area and compare to other microarray data sources Once data are returned to this interface, the user may: –Select individual query results and find additional metadata about each result –Select a single query result, which shows the experiment in the “visualization” panel below and displays the first “subresult” mapped to the atlas –Further filter the experiments shown in the “visualization” panel using the filter tool Additional categories from the data may be used to show and hide the results associated with those categories in the “visualization” window –“Keep” results by moving them to the “Selected Results” panel –From the “Selected Results” panel save the results to a.csv file for further analysis These may be removed from this panel by right-clicking and selecting “Remove” Want to Add: –Ability to change the color map and scale associated with any experiment in either the “visualization” or “keep” panel –Ability to “clear” results from the “Query Results” section –Simple graphs that can be generated by mapping one gene against the other for all areas (or one area vs. another for multiple genes)-not sure ready for this yet

Further Exploration of 2D image Data After Concept-based query sends 2D image data to the zViewer User will have ability to select which datasets/images they examine in closer detail and compare to others Thumbnail results are returned to the left panel –These have useful, but minimal information visible to the user, with the ability to access more metadata –The user has the ability to determine which images are shown in one of the 4 main windows –The user can clear unwanted results In the main window the user may: –Navigate and when possible zoom in on the images –Download and save some results (?not sure if this is allowed for some of our sources given this setup), or point the user to the place where they may download the image

Search by ROI (?name?) Must Open an Atlas in Stereotaxic space (MDA2006_STX.atlas default) Open Drawing Tool Delineate ROI-need control key plus mouse-more obvious way to do this? Generate Query Return Results displayed in zViewer –In the future this will need to be integrated with the Concept Query (next year)

Create my own Atlas This is advanced functionality-may wish to leave out User will load their own image data (or can use one of ours) Open the Label tool Open the Drawing Tool Create a new label volume using the volume tool Create a new label using the and label tool Delineate the area using that label Save these labels as a new label volume