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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
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
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
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/`) - [ ] 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**- [ ] 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
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
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
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
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
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
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
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- [ ] 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
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
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
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](https://atlases.ebrains.eu/viewer-staging/?templateSelected=Big+Brain+%28Histology%29&parcellationSelected=Grey%2FWhite+matter&cNavigation=0.0.0.-W000.._eCwg.2-FUe3._-s_W.2_evlu..7LIx..1uaTK.Bq5o~.lKmo~..NBW&previewingDatasetFiles=%5B%7B%22datasetId%22%3A%22minds%2Fcore%2Fdataset%2Fv1.0.0%2Fb08a7dbc-7c75-4ce7-905b-690b2b1e8957%22%2C%22filename%22%3A%22Overlay+of+data+modalities%22%7D%5D) - **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
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
Staging Checklist
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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 - [ ] WorksExplore 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). - [ ] WorksPoint 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 - [ ] WorksSaneURL 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/`) - [ ] 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**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. - [ ] WorksExploring 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 - [ ] WorksPlugin 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 - [ ] WorksSelecting 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 - [ ] WorksExploring 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. - [ ] WorksAtlas 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) - [ ] WorksDoc 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 - [ ] WorksBasic 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 `ExpectingDoc 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 - [ ] WorksDoc 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 - [ ] WorksDoc 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 - [ ] WorksAtlas 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](https://atlases.ebrains.eu/viewer-staging/?templateSelected=Big+Brain+%28Histology%29&parcellationSelected=Grey%2FWhite+matter&cNavigation=0.0.0.-W000.._eCwg.2-FUe3._-s_W.2_evlu..7LIx..1uaTK.Bq5o~.lKmo~..NBW&previewingDatasetFiles=%5B%7B%22datasetId%22%3A%22minds%2Fcore%2Fdataset%2Fv1.0.0%2Fb08a7dbc-7c75-4ce7-905b-690b2b1e8957%22%2C%22filename%22%3A%22Overlay+of+data+modalities%22%7D%5D) - **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 - [ ] WorksSwitching 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