arivis Pro VR is an image analysis software designed specifically to facilitate image analysis tasks that require manual interaction in 3D. This includes: navigation and visualization, where VR provides much more realistic depth perception; manual distance, length and angle measurements; sculping of complex 3D segments; manual tracking and other tools.
Using arivis Pro VR
Getting started with arivis Pro VR
arivis Pro VR is a Windows-based image visualization and analysis solution designed for manual interaction in virtual reality with multidimensional volumetric image datasets. It offers tools for manual segmentation and tracking along with a collaborative toolset for the mutual exploration of images in VR.
Opening images
The simplest way to open images is simply to drag and drop an image file into an open viewer. Files in the arivis SIS format will open immediately, supported files of any other format will trigger the import process which creates a SIS file.
Basic VR Controls
Once in VR, most functions are accessible directly through the VR controllers. These examples use the Oculus Touch controllers, but other supported controllers work the same way as long as they have the corresponding buttons. The main buttons are:
- Trigger: Action button activated using the index finger. This is usually used to use the various VR tools (move clipping planes, sculpt or track objects), or to interact with menu items.
- Grab: Main navigation tool activated using the middle finger. Grab and hold to move a point in space at the tip of the controller. Grab and move with both hands to adjust the position of two points in the volume relative to each other. Moving these points apart will expand the volume, moving them together will shrink the volume. This can also be used to rotate the volume.
- Left-hand joystick: Tool selection. Clicking on the joystick with your thumb will open the Tools menu. Use your right hand and the trigger to select various tools and functions. Moving the joystick left or right will switch between various modes for the current tool (e.g. add/remove objects, type of clipping mode, etc)
- Right-hand joystick: Also sometimes used to switch between other aspects of the current tool (e.g. switch objects sculpting tool shape) and to progress forward or back through a time series
- A: Accept / confirm. Used to confirm the end of the current tool executions (e.g. finish the current track, object edit, line measurement).
- B: Help. Press once to show the help menu for the current tool. Press again to close it.
- X: Cancel / Delete. Used to cancel the current action without saving changes or to delete objects (e.g. point in a line)
- Y: Quick tool change
- Menu: Opens the main settings menu. In the main menu, users can select which channels to display, adjust opacity curves, and access many other settings of the software.
Panels
Situated to the right of the viewer, the panels give the user access to tools not necessarily directly related to the VR and other functions. Some panels open automatically (navigator, Opacity Settings...), others can be opened by right-clicking in the panels and selecting the tool needed.
This guide is only intended as a basic introduction. Additional guidance, including guides for specific controllers, is available in the Help menu of the desktop application.
Setting up a collaboration session in arivis Pro VR
This article explains the principles and tools used in arivis Pro VR to set up collaboration sessions that can be shared by multiple users.
Setting up a session
Setting up a collaborative session involves setting up three specific aspects of the session: the dataset to be used and how it will be made available; settings concerning audio communications; and the participants and access.
Logging into the VR Collaboration panel
Login to the Collaboration panel. You'll see a list of sessions you have access to.
Click Add Session (green + sign) to create a new session.
In the session configuration window, you can start by entering a session topic and schedule a date/time for the session. For sessions that don't need a specific time, you can simply select Session starts immediately and the session will be ready as soon as all the other parameters are put in place.
Specifying a dataset
Any SIS file that can be used in arivis Pro VR can be used in a collaborative session.
The collaboration server works by providing a download link to a zipped folder of the SIS file and its dependencies to the clients. This file is then downloaded and unzipped automatically upon login by any user invited to the session.
There are 3 ways to make datasets available for a collaborative session:
- Publish a local image to the collaboration server
Using this method is the simplest in some ways. Just select the SIS file you wish to use and the file will be automatically zipped and uploaded to the server ready to be downloaded as users log in to the collaboration panel. However, this method limits the total zipped file size to 1GB. This includes the SIS and objects file. To use this option, simply click the Browse button to navigate to the SIS file you want to use. - Publish a local image to a shared folder
This method is similar to the first, except that the zipped file is published in a shared folder, typically on a network drive. The advantage of this method is that we are not limited to a maximum zipped file size of 1GB, however, it means that the shared folder must be accessible to all users of the session. To use this option, first, select the file you SIS file you want to use, then select the shared folder you want it uploaded to. - Link a remote image
With this method, you must have already uploaded the images you want to use as a ZIP file to a file-sharing system that offers direct download link options. For example, if using Dropbox, you can right-click on the ZIP file in the Windows Explorer if Dropbox is installed, or go to your Dropbox account in a web browser and select the option to generate a download link. When a download link is generated this way, the link may terminate in …dl=0. Changing the “0” to a “1” will enable direct downloads. Different file-sharing services work differently. Please check support pages for your preferred system to find out more about generating direct download links.
Note that this method will not work if the download requires a login or password.
Session Settings
Having specified a date, time, and dataset, the next step is selecting the session options. Mainly this is for the position of collaborators as they join the session and the audio settings if any.
The positioning can use either an “arena” style where users join the session in a circle or a “theatre” mode where collaborators join side by side.
In Arena mode, after the first user enters the session the second will join on the opposite side of the volume pedestal from the first. As more users join, they are automatically assigned to gaps halfway between those already present.
In Theatre mode, users join around a semi-circle in front of the volume pedestal.
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In either case, the Centre Distance sets how far away from the pedestal users will be when they join. Remember that users are always free to move around the virtual space as they in any normal VisionVR session, so this is only the starting point. But conversely, it is generally a good idea to make sure the users are close enough to the pedestal to interact comfortably with the data. A distance of 50cm to 1m is a good starting point for you to try.
Next, we must set the audio options. As with most collaboration scenarios in real life, the ability to communicate verbally is key to the success of the session. Collaborative sessions in VisionVR can be configured to use a Mumble server, or simply use whatever audio/video conferencing system you have available to run in parallel to the VR session. Details on how to configure Mumble are available in the Help files. If you prefer to use a remote conferencing service (e.g. MS Teams, GoToMeeting, Webex), configure your session there first then simply copy and paste the joining link in VR session settings. When users join the session, a message will pop up with the link provided for the user to follow and connect to the conferencing service. Once in the call, the user can return to the VR session with the audio session running in parallel.
Participants
The final step in configuring a collaborative session is the selection of participants.
Anyone can be invited to join a collaborative session as long as they have:
- a computer capable of running the software
- arivis Pro VR installed on their computer with an active license (contact support by creating a support ticket at the top of this page to get a download link)
- been set up as a user on the collaboration server (Contact support to have an account created)
- a compatible VR headset
Note that it is possible to join a VR collaborative session if you do not have a VR headset, though the experience will be inherently limited.
Also, while you do not need the Collaboration module on your license to join a session, you do need one to create and host a session.
To add a user to the session, simply type their user name in the first box in the Participants section then click Invite User. If the user account exists the invitation will be sent once the session creation is complete and it will appear automatically when they login to the Collaboration panel. Add more users one-by-one as above. If you then want to remove a user you can do so by selecting them in the invited user field and then click Uninvite Selected User .
Click Save when all participants have been added and all other details of the session have been confirmed.
Editing a session
If any parameters of a session need to be modified for whatever reason, you can do so at any time before the start of the session. To do so, start by selecting the session you want to edit in the Collaboration panel and then click Edit (blue pencil icon).
You will then have the possibility of editing any of the session parameters as above.
The session parameters will then updated on each participant's machine the next time they log on to the Collaboration panel on their system.
Note that changing the session dataset parameters will mean that the dataset will need to be downloaded again by the participants when they log in. Avoid making changes at the last minute to ensure there is enough time for participants to download the data prior to joining the session.
Joining a session
To join a session log in to the Collaboration panel and double click on the session you want to join.
Some points of note:
- The dataset status will update with a progress bar while the dataset is being downloaded or simply say "available" when it is ready. You cannot join a session unless the dataset is listed as available. Make sure to log in to the session with plenty of time to download the dataset. Logging in to the collaboration panel the day before a session to download any available datasets is a good idea.
- While having a VR headset is not necessary to join a session, not having one will limit the type of interactions you can have with the data. If you join without a headset you will not be able to:
- Use clipping planes, pointers or other VR tools
- Make use of the advantages of VR visualization including stereoscopic depth rendering
- However, you will still be able to hear and talk to your collaborators if you join the teleconference.
- Also, the fast, dynamic, and responsive interactions that feel natural in VR can be somewhat disorientating if looked at through a standard computer display.
Once in the session, the navigation will be fairly intuitive if you are already experienced with navigation and interactions in arivis Pro VR. VR tools can be accessed by clicking on the left-hand joystick. Tool selection is then done using the right-hand controller and trigger. If you are not the presenter you can request to present by using the A button and a prompt will appear in the current presenter's display to allow or deny the transfer of presentation rights. As a presenter you can use the normal navigation tools to move, scale or rotate the volume, use the pointer or marker tools to highlight specific features, and use clipping planes to reveal image data below the surface of the volume.
Since virtual avatars are also automatically displayed for all users who join with a headset, it is also possible for anyone to point at specific features in the virtual space and have collaborators see those interactions without the need for the presenter point and marker tools.
A chat option is also available in the Collaboration panel for users who prefer written communication or do not have the possibility of joining the teleconference.
Leaving a session
To leave a session, remove the headset and click Leave Session in the Collaboration panel.
Creating animations and exporting movies
In this article you learn how to create animations and export them as movies using the VR stories module.
Summary
- Open your image in arivis Pro VR.
- Open the Tools menu, then Toolsets, and switch to the VR Stories tool.
- Start recording by using the Trigger.
- Use the A button to store the animation path.
- Remove your VR goggles and use the VR Stories panel to review and export your animation as a movie file.
Introduction
VR provides a great environment for exploring 3D and 4D data, and sharing this environment using the Collaborative VR module in arivis Pro VR is the best way to let multiple users enjoy the same benefits of depth perception which makes VR such an asset. However, Since it is hardly practical to equip a complete auditorium with VR headsets at present, creating movies that can be easily added to presentations is probably the next best thing. Since VR provides a great way to navigate through datasets and encourages exploring viewpoints that may me be difficult to conceive using screen based 3D viewers, it is also a great environment to create such animations for export.
The VR Stories module in arivis Pro VR provides the tools needed to create animations directly in the VR environment for export as movies.
Recording animations
Notes on recording animations
The VR Stories module provides several options for creating animations. The first of these is whether to record a continuous or step by step recording. In continuous recording the user starts recording and the software automatically and continuously records the user's actions. This method is in some sense easier as there is no need for the user to actively interact with the recording process except to terminate the recording when finished. However, this method functions best if the user has already prepared what they want to show in some detail to avoid having to start over again each time a hesitation or mistake spoils the recording. therefore, some rehearsal is highly recommended.
In contrast, the step by step recording requires that the user actively records each transition step much like the storyboard works in arivis Pro. This is a little more laborious, but gives the user plenty of room to explore and refine each step in the animation to ensure the best results.
VR Stories can include changes in position and scaling of the volume, position of the clipping tool, opacity changes, changes in rendering mode, and object visibility. However, they do not include object segmentation or isosurface modifications, and generally the creation of manual measurements. If we want to record such things it may be best to use screen recording software to capture what is shown in the arivis window, which mirrors what the user sees in the glasses.
The main advantage of creating animations over just recording the screen is the ability the generate higher resolution movies than what we may be capable of displaying in the headset.
As mentioned in our VR introduction page, one key aspect of creating a useful and comfortable VR experience is the ability to render high quality renderings very rapidly through the headset. This is the main reason that arivis VR requires a desktop GPU based rendering. But even with powerful desktop GPUs some compromises must be made to render quality and resolution to guarantee a fast frame rate, more so for large datasets (typically anything larger than 1000x1000x1000 pixel equivalent). But while a high frame rate is clearly important while the users is wearing a headset, once an animation is recorded we can usually afford taking a little more time to generate a movie of higher quality from the animation when the user is no longer wearing the headset. If using screen recording software there is no option to generate higher quality movies than what is visible in the headset. However, exporting animations as movies does provide the option to generate higher resolution renderings.
Recording an animation in VR, especially when in continuous mode, is quite similar to recording footage using a hand-held camera. The continuous recording smoothes out the movement by sampling the position every second, but care should be taken to minimize head movements when recording.
Also, because the VR experience is generally quite fluid, adept users can tend to navigate rather quickly through their datasets, and while this feels very natural with the headset on, it can leads to animations that are much too fast for an outside viewer to follow. Therefore, when recording animations it is recommended to:
- take your time
- avoid fast and/or wide movements
- pause regularly to allow your audience to focus on what you want to show them
- remember that the controllers are not visible in the exported video so they cannot be used to point at specific structures or objects
- use object visibility filters from the main menu to allow your audience to focus on specific objects as needed
Accessing the VR Stories tools
Creating an animation with continuous recording
To create an animation in continuous mode, start by opening the tools menu. Go to the Recording tools and select the CONT option. Then, use the trigger to start recording. Record your animation then press the A button to finish recording.
Creating an animation with step-wise recording
Creating an animation in step-wise mode is very similar, in that we start by clicking the trigger button and still use A to terminate the recording, but we must also press the trigger for each additional keyframe.
Example Recording
Exporting animations as movie files
Movie Style
Framerate
A movie file is a series of individual frames which, when played in sequence, produce an animation. The higher the frame rate the smoother the animation will appear, but the file will also be much larger, require a lot more time to produce, and potentially require high-end hardware to playback (double the framerate > double the file size > double the rendering time > double the playback resource usage).
A framerate of 30FPS is usually fine for most uses, but 60FPS may be preferable for 360 degree videos (see below).
A lower framerate will render much faster and may be used to check the animation export before rendering the movie again with higher framerate and resolution settings for production.
Resolution
Quality
The quality setting is most important for large volumes, ut generally has a big impact on the processing time. The quality setting goes from Very Low to Very High and each increase in quality level results in both an increase in the quality of the video render and the processing time needed to produce the video file.