Tutorials

Unlike snapshots and HD image exports that can normally be stored in memory for easy copy & paste into an output destination (e.g. PowerPoint presentation), movies are generally much larger and therefore need to be written to the hard disk and so the first options we find relate to the save location and name. The save location and name are completely up to you (the default is to save the movie with the same name as the original file in the same folder as the dataset). For the video format we need to consider where the video will be shown. Generally most modern devices support the H264 format and it is our recommendation. It is also a good format for importing into video editing software if we want to splice our arivis video with other footage, but some older systems may not support it and MPEG4 may be more suitable in such cases. 

After the file saving settings we have the movie video output options. These can make a significant impact on the quality of the video output and the time required to create it.

Generally speaking, the higher the quality of the video the longer the movie export will take. 

The Video Resolution setting affects both the size of the output file and the quality of the output. Here the the way the video will be presented will be quite important. If we include the video in a PowerPoint presentation, using the XGA or HD (720p) options are usually fine, especially if the video does not take the entire slide. If we export it for full screen viewing then Full HD (1080p) up to Ultra HD (4K) may be preferrable, but we should remember that the time it takes to render the video will increase significantly, and so will the output file size, for what may appear to be only a marginal gain in image quality in many cases. For example, going from 1080p to 4K will typically double the rendering time. arivis also support 360 video outputs which can be quite interesting in some cases, but requires viewers that support this format and some user interactivity to set the view angle when playing back the video.

The frame rate affects how smooth the video playback can be. Low frame rates (below 24FPS) can appear a little jerky, while 25-30FPS is the standard for most videos. Using 60FPS can appear smoother, and is recommended for 360 videos, but some video players won't be able to play back these high framerates smoothly resulting in noticeable jumps as the media player lags and then catches up to the required framerate. The most important thing to note is that going from 30FPS to 60FPS will require at least twice as much time to process the video and will result in a file that is about twice as large. 

Generally, we recommend using a low video resolution and framerate (720p at 25FPS) to produce a video quickly, and switch to high resolution and higher framerates only on occasions to really showcase data only as needed.

This setting is mostly related to how the software handles large datasets. By large datasets we mean datasets for which a single timepoint cannot easily fit in the video memory of the GPU.

Viewing data in 3D and rendering videos are both highly dependent on the GPU. We cover the topic of how arivis handles large data in the 4D viewer in this article, but in short, since most GPUs have a finite amount of video memory available and a finite ability to render 3D datasets within a given amount of time, arivis typically down-samples data to make possible to render quickly in 3D. This down-sampling can lead to a noticeable drop in in the level of detail we can render and can also lead to noticeable down-sampling artefacts. As we explained in this article about rendering HD screenshots, it is always possible to render both screenshots and videos with the highest level of details, but for large datasets this comes at the cost of high processing times.

The data resolution slider adapts both to the PC configuration and to the dataset.

The scale goes from 64MB of VRAM usage on the left to the full resolution of the dataset on the right, and each graduation mark typically represents a doubling of the memory usage.

Note that since the 3D viewer renders 8bit version of the images the VRAM requirement may be significantly smaller than the actual dataset. Also, since we can only render one timepoint in any given frame, the amount of memory required is limited by the amount of data in a single timepoint.

The colour coding reflects the hardware configuration. The green part of the scale represents the amount of VRAM available on the GPU. Sticking to the green part of the scale reduces the loading times and also leads to much faster renders.

Since most computers typically have more system memory that video memory, we can use this as temporary storage for the image data instead, up to the amount of system memory available. The loading time is usually comparatively faster because loading 1MB from the disk in the RAM is usually faster than loading that data in the VRAM, but the rendering time suffers because the GPU is now reading data from the RAM rather than the faster and closer VRAM.

But since some datasets can be larger than even the RAM available, arivis also allows creating high resolution videos even at native resolution by using a hybrid rendering approach, though this is done at the cost of rendering time. 

If we are rendering a very large dataset, it is recommended the minimum amount of data resolution required to see the detail that we need to see. Some experimentation using HD screenshots may be worthwhile to find out what those optimal settings might be. It may also be worth considering splitting the animation into several movies and using volume clipping to narrow down the rendering to specific regions of interest for the high level of detail required and then, if necessary, merging the movies into a single file using video editing software.

Inputs: Select the TAGs of the structures to be compartmentalize.

The top list shows the reference TAG , while the other lists show the children TAGs. By default, 2 hierarchical levels are provided.

Additional children can be added using the + Add input

Move the selected TAG as a "child" of the above TAG and push it down in the hierarchy.

Move the selected TAG to the same level of the above TAG and push it up in the hierarchy.

Open the Tag relationship panel. From this panel, various options can be defined.

The following options (rules) are available:

Child object must be completely inside the parent structure.

Check whether a "child" object is partially covered by a "parent" structure. You can set the minimum amount of overlap using either the slider or the text box.

The Min. Overlap value defines the percentage of the child object volume that must be covered by the parent structure to be considered as compartmentalized.

If you choose 0%, it still checks whether there is at least 1 voxel of coverage.

Note

The selected parent TAG, as well as the child TAG can label more objects. For any object in the Parent TAG, all the child objects are compared to it in order to establish their belonging.

Child object must be located within the max. distance value (The children distances are taken outside the parent structure only)

These 3 options can be set independently or in combination between them.

The compartment operator generates different outputs. Each of them can be enabled and named freely by the user. Multiple outputs allow to better group and distinguish between the different features available.

Main Compartment output

From the operator menu, the main compartment TAG can be renamed. By default, the TAG name is the same

Click on the colored box to change the objects colorization.

• Main Compartment TAG in the objects table
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Each parent structure reports the children belonging to it accordingly to the Compartmentalization settings.

Parents Compartment output

A new TAG collecting the parents structures can be created.Press the «Configure output» icon on the right of the parent selection.

Check ON to activate the option and type the Tag name in the text box.

Pull down the list of additional Features on the right in order to create group statistics

• Parent Compartment TAG in the objects table
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The parent structures are shown with the related teatures.

Children Compartment output

A new TAG collecting the parents structures can be created.

Press the «Configure output» icon on the right of the parent selection.

Check ON to activate the option and type the Tag name in the text box.

Pull down the list of additional Features on the right in order to create group statistics.

• Children Compartment TAG in the objects table
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All the children objects are shown with the related teatures.

Additional Children Compartment output

Additional features related to a specific relationship criteria, can be set.

• Store overlap feature: Children Overlap
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• Store overlap feature
• Saves in the objects table a custom feature reporting the children overlap ratio. The feature is available for the objects included in the «Children» compartment TAG.
• Additional «Store overlap feature» in the objects table.
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• Values in a range of 0.0 to 1.0.
• Value equal 1.0 means object fully compartmentalized.
• Note: The Store overlap feature option is available in the Edit Output dialog box only if the related criteria is ON.
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• Store distance feature: Children Distance
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• Store distance feature saves in the objects table a custom feature reporting the children distance from the parent surface. The feature is available for the objects included in the «Children» compartment TAG.
• Additional «Store distance feature» in the objects table.
• Note: The Store distance feature option is available in the Edit Output dialog box only if the related criteria is ON.
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• Provide input modes as separate Tags for statistics
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• Provide input modes as separate Tags for statistics creates new Tags grouping the children objects belonging to each of the active option described here above.
• Additional «Provide input modes as separate Tags for statistics» in the objects table.
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Each Compartments operation can have one Parent object tag and multiple children object tags. If there are several potential parent objects in your pipeline, either multiple Compartments operations must be used (one for each parent type), or the parents must be given a common tag with the Combine Segment Outputs operation. The tag to be used for the parents can be selected from previous pipeline tags. 

Parents can have multiple children tags. When added to the pipeline the operation starts with one parent and one child tag. To add another child object tag we can just click "+ Add input" and select from the available object tags. Note that the children cannot be either the parents or a subset thereof.

Once the children have been selected we need to configure by what criteria children can be included. This is done by clicking the relation icon:

Then we can select under what conditions objects can be considered a child of any given parent:

If the Inside rule is selected, any potential child object that is fully within the boundaries of the parent will be included.

If the Intersecting rule is selected, a child that crosses the boundary of the parent can be included, depending on the amount of overlap between the parent and child candidate, as defined by the Min. Overlap slider.

If the Close rule is selected, potential children can also be included based on the proximity of these objects to potential parents. Note that children can only belong to one parent so if a child is within the max allowed distance of two parents it will be assigned to the closest one.

Of course, in many cases, the number of children is a very valuable metric in itself, but in many cases, more interesting insight can be had from more specific measurements. for example, if there are multiple potential children types it might be more interesting to get the number of children of each type separately or measure the numerical density of objects within each parent.

However, many of these features are not available within the standard feature set since they wouldn't make sense in many cases that don't involve compartmentalization. Instead, we must create new Custom Features. To do this, we open the Custom Features window directly from the Objects menu or from the feature selection window in the Objects table:

In the Custom Features Window we can then add a new Custom Feature:

Examples of useful Custom Features include:

• Numerical Density - This is a Compute feature reporting the Ratio of # Children to Volume
• Specific Children Count - An object count feature linked to a specific object tag
• Children Volume Statistics - A Group Statistics feature of the volume of children in a group.

.. and many combinations thereof (Volume ratio, tag specific numerical density, etc).

Along with Custom Features, the objects table layout can also be changed to provide easier access to the features of parent and children.

The default layout for the Objects table is a single table showing all the objects with the selected tags. If the Compartments operation has just been run it may look something like this:

However, in this layout, the table doesn't give any clear indication of which objects are parents and which are children, or the relationship between them. Instead we can switch to the Master/Detail layout where parents can be displayed on the top, and the respective children shown in their own table at the bottom:

In the Master detail layout, each table behaves somewhat independently, meaning that different tags can be selected at the top and bottom, but the Detail table only shows the children of parents selected in the Master table. 

Of course, the objects table is a powerful tool for visualizing and sorting the results of the Compartments operation. However, in many cases, it can be advantageous to export the results so that further analysis of the results can be done in different software like Excel. In that case, the results can be exported, either out of the Objects table using the Im/export button, or directly in the pipeline by adding the Export Objects Features operation.

The Export Object Features operation can be configured in a variety of ways, including the Master-Detail report as seen above.

As with the Master-Detail layout in the objects table, the features to be exported can be set independently for both the main table export and the details tables.