Tool: ScholAR

Schol-AR is a website and associated software that allows users to create augmented reality overlays for their publication images. Users can create a Schol-AR account free of charge and upload 3D models from ChimeraX, which can then be linked to figures in a publication for viewing the associated 3D augmentations with a smartphone or web-based PDF viewer. Schol-AR is described in:

Integrating data directly into publications with augmented reality and web-based technologies – Schol-AR. Ard T, Bienkowski MS, Liew S, Sepehrband F, Yan L, Toga AW. Sci Data 9(1):298 (2022).

See also: Schol-AR YouTube videos

The ChimeraX ScholAR tool interfaces with the Schol-AR website to allow:

• creating a user account
• for a user, creating one or more projects, each corresponding to a single publication, poster, or presentation
• within a project, creating one or more augmentations, each consisting of a 3D model to show in augmented reality and the corresponding target image that appears in the project (e.g., a figure in the paper)
• generating QR codes for each project:
  • a permanent, public QR code that should be included in the publication, poster, or presentation so that viewers can access the associated Schol-AR augmentations
  • a private QR code that acts like a password to edit the project; it should be kept private and is not guaranteed to be permanent

Deleting an augmentation or project (if desired) should be done at the Schol-AR website. After that happens, the local copies of the associated files can be removed by choosing Clean Project Files from the context menu of the ScholAR tool.

The ScholAR tool is also implemented as the scholar command. See also: save

Schol-AR Login
Project Specification
Augmentations

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Schol-AR Login

The ScholAR tool can be opened from the General section of the Tools menu and manipulated like other panels (more...). The initial panel is for logging in to Schol-AR.

Users who do not yet have a Schol-AR account should first go to the Schol-AR website, register for an account, log in to the account, go the Profile settings, and then click “Get API Token.” The username, password, and API token should be noted down for future access to the account.

• Users who have already logged in to Schol-AR on the current device can simply choose their existing local username from the drop-down menu, then click Select Existing User.

• Users who have not yet logged in to Schol-AR on this device should Create New User by entering the following and clicking Submit:
  
  
  • Username – a local username to be used by ChimeraX as a convenient alias to the API token; this does not need to be the same as the username at the Schol-AR website

    The local username and any other strings input to this tool must not contain any characters other than letters, numbers, and spaces.

  • API Token – the API token obtained from the Schol-AR website as described above

A successful login switches the panel to the projects section.

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Project Specification

An existing project (if any) can be specified by choosing its title from the dropdown menu and clicking Select.

Alternatively, a new project can be specified by entering a title etc. and clicking Create:

• Project Title (*required)
• Project Type (*required), with choices:
  • Scientific Paper
  • Poster or Other Presentation
  • Book or Chapter
  • Other
• Project URL (optional) – link to publication or institute

Specifying a project switches the panel to the augmentations section. Other buttons:

• View at Schol-AR.io – go to the user account at the Schol-AR website
• New Login – return to login

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Augmentations

A new augmentation (a 3D model in GLB format) can be created from the current contents of the ChimeraX scene by giving it a name and clicking Create New. A current limitation is that the GLB file size cannot exceed 30MB. Alternatively, an existing augmentation (if any) to modify can be specified by choosing its name from the dropdown menu and clicking Select.

Specifying an augmentation shows its target image and additional buttons for for modifying the augmentation:

• Update Target Image – update the target image in the thumbnail and at the Schol-AR website
  
  

  The target image must match that in the media seen by the viewers (e.g., the corresponding publication figure), so it is very important not to accidentally update/overwrite it when the appearance in ChimeraX is different. There is no way to recover the previous target image with the ChimeraX ScholAR tool, scholar command, or at the Schol-AR website. If the target image no longer matches the published image, others will no longer be able to view the associated augmentation.

  
  
• Update Model – update the 3D model at the Schol-AR website; a current limitation is that the file size cannot exceed 30MB
• Preview – open a separate window displaying a larger version of the target image and the two QR codes for the project, to allow previewing the augmentation with a mobile device
• Save Files Locally – open a file browser to save the augmentation target image, augmentation 3D model file, and the public QR code for the project
• Save and Close – save a ChimeraX session and close the current session (this also occurs whenever the user navigates to a different section of the dialog, such as by using the buttons below)

Other buttons:

• View at Schol-AR.io – go to the user account at the Schol-AR website
• New Login – return to login
• Projects ‐ return to projects
• Augmentations – return to choosing an augmentation
• Store QR – open a file browser to save the public QR code for the project