Volume 41 (2022), Number 3

Eurographics Conference on Visualization (EuroVis) 2022
R. Borgo, G. E. Marai, and T. Schreck(Guest Editors)

Barrio: Customizable Spatial Neighborhood Analysis andComparison for Nanoscale Brain Structures- Supplementary Material Jakob Troidl1,3 , Corrado Cali2 , Eduard Gröller3 , Hanspeter Pfister1 , Markus Hadwiger4 and Johanna Beyer1
1 Harvard University, 2 University of Turin, 3 TU Wien, 4 KAUST

Figure 1: Analysis views generated for ST3: Mitochondric spine
coverage. (a) to (c): low-, medium-, high-cardinality comparison
views. (a) detailed spine visualization for a single dendrite basedon a lollipop chart. Each lollipop encodes the length (bar height)
and volume (circle size) of a spine and indicates its position in relation to the mitochondria (blue horizontal bars) of the dendrite,(b) dendrite abstraction showing one green bar per dendrite. We
depict spines as horizonal lines with their vertical position indicating their position along the dendrite and mitochondria (blue). (c)scatter plot of 26 mitochondria, showing their spine coverage.

1. Case Study: Mitochondria AnalysisBelow, we describe the third scenario subtask of the “MitochondriaAnalysis” case study described in the paper.
1.1. Mitochondric Spine Coverage (ST3)
Domain Goal: In the final scenario subtask, the scientist wanted
to study the relationship between dendritic spines and mitochondria. Spine coverage is defined as a mitochondrion being present
in the cell region right below the neck of a spine. Spines often develop synapses, which are big energy consumers. Therefore, knowing more about mitochondria close to spines plays a vital role inunderstanding metabolic processes. Furthermore, the presence ofmitochondria might influence spine plasticity, which in turn may
influence fission/fusion dynamics of mitochondria.
Visualizations: Fig. 1 shows the visualizations for analyzing dendritic spines. For low-cardinality comparisons we developed a customized spine visualization based on lollipop charts and integrated
it into Barrio. We abstract the dendrite to a straight horizontal line
in 2D (see Fig. 1a), inspired by Neurolines [AABS∗ 14]. Next, we© 2022 The Author(s)Computer Graphics Forum © 2022 The Eurographics Association and JohnWiley & Sons Ltd. Published by John Wiley & Sons Ltd.

encode the mitochondrion position (blue shapes) within the dendrite and represent spines and their lengths as green vertical lines.
The red circle on the top of the spine represents a synapse, andits radius encodes the spine’s surface area to volume ratio, which
gives an intuition of the spine’s shape. This view provides a detailed
analysis of the dendrite’s morphology (i.e., mitochondria positions,spine locations, and synapse sizes). In the medium-cardinality comparison mode, each dendrite is represented as a vertical rectangle(Fig 1b), allowing the comparison of up to a dozen dendrites ina single visualization. The height of the rectangle represents thelength of the dendrite and the positions of the mitochondria withinthat dendrite are visualized through the smaller blue rectangles.
Spine positions are indicated as black horizontal lines. For highcardinality comparisons, the scientist defined a scatterplot in theADF file (Fig 1c). Each data point corresponds to an individual
mitochondrion. The horizontal axis encodes the number of spines
covered by this mitochondrion, and the vertical axis encodes themitochondrion’s volume.
Interactive Analysis: The domain expert started by analyzing multiple mitochondria and dendrites and immediately observed thatspines usually develop with mitochondria coverage. To follow up
on this initial insight, he selected six mitochondria to compare
them. In a particular case, he observed two mitochondria that overlapped in the dendrite. He speculated that these two mitochondria
might initially have been a single mitochondrion that split into twoparts. He pointed out that he wants to use Barrio in the future to analyze whether regions of overlapping mitochondria develop morespines. When switching to the scatterplot visualization, our collaborator immediately spotted a linear dependence between the mitochondria volume and the number of spines covered, which was a
new finding for him. This observation indicates that mitochondria
coverage plays a vital role in spine development.

2. Examples of Analysis Definition Files
In this section, we give two examples of analysis definition files(ADFs). Figure 2 shows the ADF used in the case study. It defines
three scenario subtasks that all use mitochondria as target types.
Figure 3 gives an example of an ADF comparing two data sets

J. Troidl / Barrio

Figure 2: The analysis definition file (ADF) for the case study "Mitochondria Analysis" specifies three scenario subtasks (ST1: Synaptic
neighborhood of mitochondria, ST2: Mitochondria placement, and ST3: Spine coverage of mitochondria). Each scenario subtasks supports
visual comparison at three comparison cardinalities by defining a specific visualization method for each level. Each visualization method isdefined by a set of parameters and data mapping.

© 2022 The Author(s)Computer Graphics Forum © 2022 The Eurographics Association and John Wiley & Sons Ltd.

J. Troidl / Barrio

Figure 3: An example of an analysis definition file with multiple
data sources and synapses as target types. The analysis scenario"Relation of synapses and mitochondria" defines one scenario subtask (ST1: Surrounding mitochondria) and uses synapses as targettypes. In this task, scientists can compare synapses of two different
data sets to investigate neuronal development over time.

("mouse2" and "mouse3"). Here, the analysis scenario defines only
one scenario subtask using synapses as target types. More details
and information about supported visualization types and a detailed
documentation can be found on our website [VCG22].
3. High-Resolution Figures
Below, we provide high-resolution versions of the figures in ourpaper (see Fig. 4, Fig. 5, Fig. 6, Fig. 7, and Fig. 8).
References[AABS∗ 14] A L -AWAMI A., B EYER J., S TROBELT H., K ASTHURI N.,
L ICHTMAN J. W., P FISTER H., H ADWIGER M.: NeuroLines: A Subway Map Metaphor for Visualizing Nanoscale Neuronal Connectivity.
IEEE Transactions on Visualization and Computer Graphics 20, 12(2014), 2369–2378. doi:10.1109/TVCG.2014.2346312. 1[VCG22] VCG: Barrio Documentation, 2022. last accessed: 04/17/2022.
URL: https://github.com/VCG/Barrio/wiki. 3© 2022 The Author(s)Computer Graphics Forum © 2022 The Eurographics Association and John Wiley & Sons Ltd.

J. Troidl / Barrio

Figure 4: High resolution version of Figure 5 in the paper. Scalable comparisons at three different cardinalities. Low-cardinality comparisons (top row) analyze a small number of spatial neighborhoods and use juxtaposed small multiples. Medium- and high-cardinality
comparisons support increasingly larger numbers of neighborhoods and encode a single neighborhood as a single visual element (i.e., aviolin in a violin plot) or a single visual mark (i.e., a dot in a scatterplot), respectively.

Figure 5: High resolution version of Figure 6 in the paper. Detailed 3D neighborhood view. The dendrite (green) and close synapses (red).
(a) 2D slice overlay of the original EM data to show biological context. (b) Silhouette enhancing and semi-transparent surface rendering tohighlight how enclosed mitochondria (blue) are positioned within the dendrite. (c) Color-coding of a mitochondrion showing the distance
between the mitochondrion and its surrounding cell membrane.

© 2022 The Author(s)Computer Graphics Forum © 2022 The Eurographics Association and John Wiley & Sons Ltd.

J. Troidl / Barrio

Figure 6: High resolution version of Figure 7 in the paper. Analysis views generated for ST1: Synaptic neighborhood of mitochondria. (a)to (c): low-, medium-, and high-cardinality comparison views. (a) distance tree for mitochondrion ’Mito 1’ showing its surrounding synapses(red) and their closest mitochondria (blue), (b) bar chart showing three mitochondria and the spatial distance of their surrounding synapses,(c) distance matrix of all mitochondria and their neighboring synapses.

Figure 7: High resolution version of Figure 8 in the paper. Analysis views generated for ST2: Mitochondria placement. (a) to (c): low-,
medium-, high-cardinality comparison views. (a) cumulative histogram showing the percentage of a single mitochondrion’s surface that iswithin a certain distance to the surrounding cell membrane (red means close, blue means far), (b) violin plots for four mitochondria, eachshowing the distance distribution of the mitochondrion’s surface to the surrounding cell membrane (color and vertical position encode thedistance, the width of the plot encodes the number of surface points with that distance), (c) scatter plot showing many mitochondria (dots)
and their volume correlated to their distance to the cell membrane.

© 2022 The Author(s)Computer Graphics Forum © 2022 The Eurographics Association and John Wiley & Sons Ltd.

J. Troidl / Barrio

Figure 8: High resolution version of Figure 9 in the paper. Comparing synapse locations in two different mouse data sets (purple andgreen). The 3D views show the four selected mitochondria neighborhoods. Grouped bars show the distances between mitochondria and theirneighboring synapses. Hovering over a bar highlights the corresponding synapse in the 3D neighborhood view (orange). The young mouse(green, right) exhibits a wider mitochondria-synapses distance bandwidth than the adult mouse (purple, left), indicating synaptic pruningover time.

© 2022 The Author(s)Computer Graphics Forum © 2022 The Eurographics Association and John Wiley & Sons Ltd.