v2.14.6

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Doc User Interface Structure

From doc - User Interface Structure

User can expand coordinate view

• Given User launched the atlas viewer

• Given User selects an atlas, parcellation, parcellation

• When User clicks [chevron-down] button

• Then The coordinate view expands

• Works

User can enter custom coordinates

• Given User launched the atlas viewer

• Given User selects an atlas, parcellation, parcellation

• When User clicks [pen] button

• Then User can directly enter/copy/paste/select MNI coordinates

• Works

User can select via atlas selection panel

• Given user launched the atlas viewer

• Then User should have access to atlas selection panel at the bottom of the UI

• Works

User can search for regions

• Given User launched the atlas viewer

• Given User selects an atlas, parcellation, parcellation

• Given User minimized side panel

• When User clicks [magnifiying glass] and then focus on the input box

• Then User can type keywords to search for regions

• Works

User accesses help panel

• Given User launched the atlas viewer

• When User clicks the [circled-question-mark] button

• Then A modal dialog about keyboard shortcuts, terms of use and so on should be visible

• Works

User downloads current view

• Given User launched the atlas viewer

• When User clicks the [download] button

• Then A zip file containing current view is downloaded

• Works

User accesses tools

• Given User launched the atlas viewer

• When User clicks the [apps] button

• Then User should see tools available to them, including screenshot, annotation, jugex

• Works

User signs in using ebrains credentials

• Given User launched the atlas viewer

• When User clicks the [account] button

• Then User should be able to sign in with ebrains credential

• Works

• All Checked

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Exploring the selected region

User should be able to explore the selected region

User selecting a region of interest

• Given User launched the atlas viewer

• Given User selected Julich Brain v3.0.3 in ICBM 2007c nonlinear space

• When User clicks a parcel

• Then The clicked parcel is selected

• Works

User navigates to the selected region

• Given User selected a region of interest

• When User clicks Centroid button

• Then The viewer navigates to the said centroid of the region

• Works

User finding out more about the selected region

• Given User selected a region of interest

• Then The user can find description about the region

• Works

User accesses the doi of the selected region

• Given User selected a region of interest

• When User clicks DOI button

• Then A new window opens for the said DOI

• Works

User searches for related regions

• Given User selected a region of interest (4p left, Julich Brain v3.0.3, MNI152)

• When User clicks Related Region button

• Then Related region modal shows previous/next versions, as well as homologeous regions

• Works

• All Checked

---

Doc Launch and Quicktour

From doc - Launch and Quicktour

Accessing quicktour on startup

• Given User first launched siibra-explorer

• Then User should be asked if they would like a quick tour

• Works

Accessing quicktour on return

• Given User launched siibra-explorer second time

• When User hit ? key or clicks (?) button (top right)

• Then User should be able to find Quick Tour button at the modal dialog

• Works

• All Checked

---

SaneURL a.k.a. URL shortener

SaneURL should continue to function.

User navigates to SaneURL UI

• Given User launched the atlas viewer

• Given User selects an atlas, parcellation, parcellation

• When User expands navigation submenu, clicks [share] button, clicks Create custom URL button

• Then User should see the SaneURL UI

• Works

SaneURL UI should be informative

• Given User navigated to SaneURL UI

• Then User should see that links expire if they are not loggedin

• Then User should see the links they potentially generate (e.g. https://atlases.ebrains.eu/viewer-staging/go/<link>)

• Works

User attempts to generate existing saneurl

• Given User navigated to SaneURL UI

• When User enters human

• Then User should be informed that the shortlink is not available

• Works

User attempts to use illegal characters

• Given User navigated to SaneURL UI

• When User enters foo:bar

• Then User should be informed that the shortlink is not legal

• Works

User attempts to generate valid saneurl

• Given User navigated to SaneURL UI

• When User enters x_tmp_foo

• Then User should be informed that the shortlink is available

• Works

User generates a valid saneurl

• Given User navigated to SaneURL UI

• When User enters x_tmp_foo and clicks Create

• Then The short link will be created. User will be informed, and given the option to copy the generated shortlink

• Works

Generated shortlink works

• Given User generated a valid saneurl

• When User enters the said saneURL to a browser

• Then They should be taken to where the shortlink is generated

• Works

Permalink works (Big Brain)

• Given https://atlases.ebrains.eu/viewer-staging/saneUrl/bigbrainGreyWhite

• Then Works

• Works

Permalink works (Juclih Brain in Colin 27)

• Given https://atlases.ebrains.eu/viewer-staging/saneUrl/julichbrain

• Then Works

• Works

Permalink works (Waxholm v4)

• Given https://atlases.ebrains.eu/viewer-staging/saneUrl/whs4

• Then Works

• Works

Permalink works (Allen CCFv3)

• Given https://atlases.ebrains.eu/viewer-staging/saneUrl/allen2017

• Then Works

• Works

Permalink works (MEBRAINS)

• Given https://atlases.ebrains.eu/viewer-staging/saneUrl/mebrains

• Then Works

• Works

Permalink works (contains annotations)

• Given https://atlases.ebrains.eu/viewer-staging/saneUrl/stnr

• Then Works

• Works

VIP link works (human)

• Given https://atlases.ebrains.eu/viewer-staging/human

• Then Works

• Works

VIP link works (monkey)

• Given https://atlases.ebrains.eu/viewer-staging/monkey

• Then Works

• Works

VIP link works (rat)

• Given https://atlases.ebrains.eu/viewer-staging/rat

• Then Works

• Works

VIP link works (mouse)

• Given https://atlases.ebrains.eu/viewer-staging/mouse

• Then Works

• Works

• All Checked

---

Navigating the viewer

Users should be able to easily navigate the atlas

User launches the atlas viewer

• When User launches the atlas viewer

• Then The user should be directed to Human Multilevel Atlas, in MNI152 space, with Julich Brain 3.0 loaded

• Works

On hover shows region name(s)

• Given User launched atlas viewer

• Given User navigated to Human Multilevel Atals, in MNI152 space, with Julich brain 3.0 loaded

• Given User has not enabled mobile view

• Given The browser's width is at least 900px wide

• When User hovers over non empty voxel

• Then Label representing the voxel should show as tooltip

• Works

User wishes to hide parcellation

• Given User launched atlas viewer

• When User clicks the [eye] icon

• Then Active parcellation should hide, showing the template

• Works

User wishes to hide parcellation via keyboard shortcut

• Given User launched atlas viewer

• When User uses q shortcut

• Then Active parcellation should hide, showing the template

• Works

User wishes to learn more about the active parcellation

• Given User launched atlas viewer

• Given User selected Julich Brain v3.0.3

• When User clicks [info] icon associated with the parcellation

• Then User should see more information, including name, desc, doi.

• Works

User wishes to learn more about the active space

• Given User launched atlas viewer

• Given User selected ICBM 2007c nonlinear asym

• When User clicks [info] icon associated with the space

• Then User should see more information, including name, desc, doi.

• Works

• All Checked

---

Doc Exploring 3D Parcellation Maps

Accessing to atlas selection panel

• Given User launched siibra-explorer

• Then User should have access to atlas selection panel

• Works

Accessing volumetric atlases

• Given User launched siibra-explorer

• When User selects multilevel human atlas, big brain template space

• Then User should see four panel volumetric atlas viewer

• Works

Zooming the volumetric atlas

• Given User is accessing a volumetric atlas

• When User scroll the wheel

• Then the view should zoom

• Works

Panning the volumetric atlas

• Given User is accessing a volumetric atlas

• When User drags with mouse

• Then the view should pan

• Works

Oblique slicing the volumetric atlas

• Given User is accessing a volumetric atlas

• When User drags with mouse whilst holding shift

• Then the view should rotate

• Works

Accessing the atlas viewer on 2D viewer

• Given User is accessing a volumetric atlas

• When User hovers, and clicks [maximize] button

• Then The specific panel will maximize, with 3D view as a picture-in-picture view

• Works

Cycling 2D view

• Given User is accessing the atlas viewer as a 2D viewer

• When User hits [space bar]

• Then The view rotates to the next orthogonal view

• Works

Restoring from 2D view

• Given User is accessing the atlas viewer as a 2D viewer

• When User clicks [compress] button

• Then the view restores to the original four panel view

• Works

• All Checked

---

Plugin jugex

Plugin jugex should work fine.

User can launch jugex plugin

• Given User launched the atlas viewer

• Given User selects an human atlas, Julich Brain v3.0.3 parcellation, MNI152 template

• When User expands the [App] icon at top right, and clicks siibra-jugex

• Then siibra-jugex should launch as a plugin

• Works

User can select ROI via typing

• Given User launched jugex plugin

• When User focus on Select ROI 1 and type fp1

• Then A list of suggestions should be populated and shown to the user. They can be selected either via left click, or Enter key (selecting the first in the list).

• Works

User can select ROI via scanning atlas

• Given User selected ROI1 via typing

• When User clicks [radar] button next to Select ROI 2 text box

• Then User should be prompted to Select a region. Single click on any region will select the region.

• Works

User can select genes of interest by typing

• Given User selected ROI2 via scanning atlas

• When User focuses selected genes, and starts typing (e.g. GABA)

• Then A list of suggestions should be populated and shown to the user. They can be selected either via left click, or Enter key (selecting the first in the list).

• Works

User can export notebook

• Given User selected gene(s) of interest

• When User clicks notebook button

• Then A new window should be opened, allowing the user to download the notebook, running it on ebrains labs or my binder

• Works

User can run the analysis

• Given User selected gene(s) of interest

• When User clicks run button

• Then Jugex analysis should be run based on the user's specification

• Works

Analysis should be downloadable

• Given User ran the analysis

• When User clicks the Save Button

• Then A result.json file should be downloaded

• Works

Result can be visualized on the atlas viewer

• Given User ran the analysis

• When User toggles Annotate

• Then the sample sites should be visible in the atlas viewer

• Works

• All Checked

---

Atlas data availability

Users should expect all facets of atlas to be available

User checks out high resolution Julich Brain regions

• Given User launched the atlas viewer

• When User selects Julich Brain v2.9 in Big Brain space

• Then User should find high resolution hOc1, hOc2, hOc3, lam1-6

• Works

User checks out PLI dataset from KG

• When User clicks the link curated in KG link

• Then User is redirected, and everything shows fine

• Works

User checks out Julich Brain in fsaverage

• Given User launched the atlas viewer

• When User selects Julich Brain in fsaverage space

• Then The atlas loads and shows fine

• Works

User checks out Waxholm atlas

• Given User launched the atlas viewer

• When User selects Waxholm atlas

• Then User is taken to the latest version (v4)

• Works

User finds Waxholm atlas showing fine

• Given User checked out waxholm atlas

• When User hovers volumetric atlas

• Then the label representing the voxel shows

• Works

User finds Waxholm atlas mesh loads fine

• Given User checked out waxholm atlas

• Then whole mesh loads

• Works

• All Checked

---

Atlas Download

Users should be able to download atlas

User downloads Julich Brain v3.0.3 in MNI152

• Given User launched the atlas viewer

• Given User selects Julich Brain v3.0.3 in MNI152

• When User click [download] button (top right of UI)

• Then After a few seconds of preparation, the download should start automatically. A snack bar message should appear when it does.

• Works

The downloaded archive should contain the expected files

• Given User downloaded Julich Brain v3.0.3 in MNI152

• Then The downloaded archive should contain: README.md, LICENSE.md, template (nii.gz + md), parcellation (nii.gz + md)

• Works

User downloads hOc1 left hemisphere in MNI152

• Given User launched the atlas viewer

• Given User selects Julich Brain v3.0.3 in MNI152

• Given user selects hOc1 left hemisphere

• When User click [download] button (top right of UI)

• Then After a few seconds of preparation, the download should start automatically. A snack bar message should appear when it does.

• Works

The downloaded archive should contain the expected files (#2)

• Given User downloaded hOc1 left hemisphere in MNI152

• Then the downloaded archive should contain: README.md, LICENSE.md, template (nii.gz + md), regional map (nii.gz + md)

• Works

• All Checked

---

Point assignment

Users should expect point assignment to work as expected

User performs point assignment on Julich Brain v3.0.3 in MNI152 space

• Given User launched the atlas viewer

• Given User selects Julich Brain v3.0.3 in MNI152

• When User right clicks on any voxel on the viewer, and clicks x, y, z (mm) Point

• Then User should see statistical assignment of the point, sorted by map value

• Works

User inspects the full table of the point assignment

• Given User performed point assignment on Julich Brain v3.0.3 in MNI152 space

• When User clicks Show full assignment button

• Then User should see a full assignment table in a modal dialog

• Works

User wishes to download the assignment

• Given User is inspecting the full table of point assignment

• When User clicks Download CSV button

• Then A CSV containing the data should be downloaded

• Works

user performs point assignment on Waxholm v4

• Given User launched the atlas viewer

• Given User selects Waxholm atlas, v4 parcellation

• When User right clicks on any voxel on the viewer, and clicks x, y, z (mm) Point

• Then User should see labelled assignment of the point

• Works

User performs point assignment on fsaverage

• Works

User performs point assignment on Julich Brain in Big Brain

• Works

• All Checked

---

Selecting a region

User should be able to select a region

User selecting a region of interest

• Given User launched the atlas viewer

• Given User selected Julich Brain v3.0.3 in ICBM 2007c nonlinear space

• When User clicks a parcel

• Then The clicked parcel is selected

• Works

User searching for a region of interest via express search

• Given User launched the atlas viewer

• Given User selected Julich Brain v3.0.3 in ICBM 2007c nonlinear space

• When User focuses on Search for regions and types hoc1

• Then Three options (hoc1 parent, hoc1 left and hoc1 right) should be shown, in this order

• Works

User selecting branch via express search

• Given User searched for hoc1 via express search

• Given Three options (hoc1 parent, hoc1 left and hoc1 right) are shown, in this order

• When User hits Enter key

• Then Full hierarchy modal view should be shown, with the term Area hOc1 (V1, 17, CalcS) populated in the search field

• Works

User selecting node via express search

• Given User searched for hoc1 via express search

• Given Three options (hoc1 parent, hoc1 left and hoc1 right) are shown, in this order

• When User clicks hoc1 left

• Then The region hoc1 left should be selected

• Works

• All Checked

---

Doc Storing and Sharing 3D view

Taking Screenshots

• Given User launched siibra-explorer

• When User takes a screenshot with the built in screenshot plugin

• Then the screenshot should work as intended

• Works

• All Checked

---

Basic UI

User should expect basic UI to work.

User launches the atlas viewer

• When User launches the atlas viewer

• Then the user should be able to login via ebrains OIDC

• Works

siibra-explorer and siibra-api version is compatible

• When User launches the atlas viewer

• Then the user should not see the message Expecting <VERSION>, but got <VERSION>, some functionalities may not work as expected

• Works

User trying to find debug information

• Given User launches the atlas viewer

• When User navigates to ? -> About

• Then The git hash matches to that of HEAD of staing

• Works

• All Checked

---

Doc Multimodal Data Features

Finding data features linked to 3D view

• Given User launched siibra-explorer

• Given User selected Big Brain space

• Then User should find >0 spatial features

• Works

Inspect spatial data feature

• Given User found data features linked to 3D view

• When User clicks on one of the features

• Then User should be shown the VOI interest, teleported to the best viewing point

• Works

• All Checked

---

Exploring features

User should be able to explore feature panel

User exploring the features related to a region of interest

• Given User launched the atlas viewer

• Given User selected Julich Brain v3.0.3 in ICBM 2007c nonlinear space

• Given User selects a region of interest (hOc1 left hemisphere)

• When User clicks the Feature tab

• Then Feature panel of region of interest is visible

• Works

User checking out a feature

• Given User is exploring features related to region of interest

• When User expands a category, and clicks a feature

• Then Feature side panel will be opened

• Works

User finding out more about selected feature

• Given User checked out a feature

• Then User can see description related to the selected feature

• Works

User checking out the DOI of the selected feature

• Given User checked out a feature (category=molecular, feature=receptor density fingerprint)

• When User clicks DOI button

• Then A new window opens for the said DOI

• Works

User downloads the feature

• Given User checked out a feature

• When User clicks Download button

• Then A zip file containing metadata and data is downloaded

• Works

User checking out feature visualization

• Given User checked out a feature (category=molecular, feature="receptor density profile, 5-HT1A")

• When User click the Visualization tab

• Then The visualization of the feature (cortical profile) becomes visible

• Works

User checking out connectivity strength

• Given User checked out a feature (category=connectivity)

• When User click the Visualization tab

• Then The probabilistic map hides, whilst connection strength is also visualized on the atlas

• Works

User quitting checking out connectivity strength

• Given User checked out connectivity strength

• When User unselects the feature

• Then The connection strength color mapped atlas disapepars, whilst the probabilistic map reappears.

• Works

• All Checked

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Explore region hierarchy

User should be able to explore region hierarchy

User exploring region hierarchy

• Given User launched the atlas viewer

• Given User selected Julich Brain v3.0.3 in ICBM 2007c nonlinear space

• When User clicks [site-map] icon

• Then The full hierarchy modal view should be shown

• Works

User are given search context

• Given User are exploring region hierarchy

• Then User should see the context of region hierachy, including atlas, parcellation and template

• Works

User searches for branch

• Given User are exploring region hierarchy

• When User searches for frontal lobe

• Then User should see the parent (cerebral cortex), the branch itself (frontal lobe) and its children (e.g. inferior frontal sulcus).

• Works

• All Checked

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Switching Atlas, Parcellation, Template

User should be able to freely switch atlas, parcellation and templates

User switches template

• Given User launched the atlas viewer

• Given User selected Julich Brain v3.0.3 in ICBM 2007c nonlinear space

• When User selects Big Brain template

• Then User should be taken to Julich Brain v2.9 in Big Brain space

• Works

User switches parcellation

• Given User launched the atlas viewer

• Given User selected Julich Brain v2.9 in Big Brain space

• When User selects Deep fibre bundle parcellation

• Then User should be taken to Deep fibre bundle in MNI152 space

• Works

• All Checked

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