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Navigating VMD

Below is a step-by-step guide to navigating the virtual microscopy database.

STEP 1: BECOME A VMD USER

Access to the Virtual Microscopy Database is free with VMD user status and will allow you to search, access and download slide files from the database of virtual slides, as well as upload your own collection of virtual image files. To become a VMD user, simply go to the subscribe page and fill out the form. Your application will be reviewed by the site administrators for approval and you will receive an email notification. You must have an affiliation with an educational or research institution as a researcher or educator in order to become a VMD user. If you have any questions about whether you are eligible to become a VMD user, please feel free to e-mail the VMD administrators at info@virtualmicroscopydatabase.org.

STEP 2: HOW TO BROWSE THE COLLECTIONS

Once you receive a notification (by e-mail) that your VMD user status has been approved, click on the VMD user login button on the upper right of the website page and login using your username and password.

After you login, you will notice that a second menu bar (light blue) will be activated below the main menu, and the VMD slide database will open.

Accessing the Slide Database: By default, when you login, the slide database page opens. Notice that the left side of the screen includes a menu that lists Tracked Directories and Collections. The right side of the screen shows thumbnail images of slides available in the active collection.

Tracked Directories are where slides that you upload will be located. See STEP 4. No tracked directory will be visible unless you have uploaded and donated virtual slide files to the VMD.

The Collections list contains folders that house each collection available in the database. Many collections contain subfolders which can be opened or closed by clicking on the arrows next to the folder names.

Thumbnail Images from each collection are displayed in the main window. You can toggle between detailed view and tiled view by clicking on the arrow next to the thumbnail pull down menu. The Detailed View is useful as it displays the filename, file size, format and any description the collection owner entered about the image.

Viewing a full size virtual slide: Clicking on the thumbnail image will open the full size virtual slide viewer. Here you can navigate around the slide, increase magnification and decide whether it is a slide you would like to download.

Downloading a full size virtual slide: Clicking on the small box (to the right or below the thumbnail depending on the mode you are viewing it in) will allow you to select the image in order to download it. Select as many of the slides that you would like (or click the select all button if you want all of them), then click the "download" icon that has now appeared on the toolbar above. The slide(s) will automatically begin downloading. (NOTE: These are VERY large files and selecting an entire database will take a significant amount of time and disk space). Please note that all image files in the VMD are published under a BY-SA-NC Creative Commons License (https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode). That means when using any of the VMD files, you will need to attribute them to the copyright holder of the image and you are not allowed to use them for commercial applications without permission from the copyright owner.

NOTE: You will need your own virtual slide viewer in order to view your downloaded files on your own computer. The viewer will need to be able to read the variety of file formats that are contained within our database. If you do not currently have a viewer (and server) for viewing virtual microscopy images, you will need to download viewer software such as the Biolucida Viewer (http://www.biolucida.net/viewer/).

STEP 3: HOW TO UPLOAD YOUR COLLECTION

We hope that you will decide to share your virtual slide collections for other database users to access. For information on the types of acceptable file formats and issues concerning copyright, please visit the Donor Information page. If you have any questions about donating your collection, you can contact us by e-mail at info@virtualmicroscopydatabase.org. Before donating, please make sure that you have permission from the copyright holder of these image files to share them under a BY-SA-NC Creative Commons License (https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode). By uploading digital image files you agree that these files are available to VMD user under these terms.

Upload images: To upload your collection, click on the upload tab located on the light blue top bar. Then click on the green "select files" button that appears. Navigate to the folder where the images you want to donate reside and click on the image or images within that folder that you wish to upload. Initiate the uploading process, which depending on Internet speed, the number of files and their size might take several minutes. The system will show the progress of the download and will display a message when the download is completed.

View your uploaded images: Once the files are uploaded you will notice that a folder with your username will appear in the "tracked directories" folder on the left side menu. If you click on your folder, you will see the slides that you have just uploaded. It may take up to half an hour until they appear. Please note that files in the “tracked directories” folder are not viewable or accessible by anyone but yourself until you make them available by following the next step (creating a collection).

Create a collection: Once you upload your images, you can create a collection folder that other users will be able to access. To create a collection, click on the "+" icon under the collections tab and name your new collection. We suggest that you use the name of your University or Organization for easy recognition. Once the collection is created, you can click the pencil icon if you would like to edit the name or description of your collection. Follow the same path to create and name subfolders in your collection folder. This way, you can create subfolders to organize your image collection by tissues and organ systems.

Move your images to your collection folder: Once you have created your collection, you can click on your tracked directories folder, choose "select all" (or select the individual images you want to share), and drag the selected files into the collection folder.

Tag/Label your images: In order for users to be able to search the VMD database and find your images, you will need to tag and describe the images in your collection folder. Please take the time to do so. In order to tag your image, click on the empty box next to or below the image thumbnail and click the "edit" button on the menu above. Within the edit mode you can select the magnification of the image, add tags and descriptions.

Removing or withdrawing your collection from the VMD: Donors have every right to withdraw or remove their slide collections from the VMD at any time for any reason. Please be advised that the files already downloaded by the users up to that point cannot be recalled. Should you wish to withdraw and remove your slide collections from the VMD, you can easily do so selecting your file folder under the Collections tab and selecting “Delete Current Collection” tab (trash can icon). Once your collection is deleted, no one will have access to your slides. In order to remove your slide collections permanently from VMD, the slides will need to be deleted from the “tracked directories” section. This can be accomplished by emailing us at info@virtualmicroscopydatabase.org.

PLEASE NOTE: You will be able to delete an image in a collection, however the image cannot be deleted from the tracked directories folder. Once an image is removed from a collection, no users other than the owner and the VMD administrators will be able to view it. If you need to remove an image from the tracked directories folder for any reason, then you must contact an administrator who can arrange for this to be done.

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