3D/4D rendering & track curation
Render volumes and curate cell tracks over time.
20 project-authored proposals · taxonomy v1.1 · 0 new benchmark runs. Verifiers and partial-credit rules below are designs, not executed results.
- Typical applications
- Imaris · napari · TrackMate
- Class GUI-need label
G2· GUI-essential
Task proposals · 20
Expand to inspect the complete original wording and proposed checks. Original proposal text remains English in both interfaces.
R08.07.01.03-T01 Render a volume as maximum intensity projection matching a reference view in napari
Original instruction
Open input/stack.tif in napari, switch to 3D view, set the display to maximum intensity projection with contrast limits [200, 3000] and the magma colormap, and orient the camera to match input/ref.png. Save output/render.png at the same size as the reference and output/camera.json (angles and zoom).
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- napari
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
drag· Drag & dropclick· Point & clickvis· Visual judgment- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
render.png SSIM ≥0.9 against ref.png; camera.json angles within 5° and zoom within 10% of the reference; the grader re-renders with the reported camera, contrast and projection, and that render must match render.png (SSIM ≥0.95). napari's IPython console is disabled and the agent has no Python shell outside the napari GUI.
Proposed partial credit
30% projection and contrast; 45% camera orientation (SSIM); 25% saved state.
R08.07.01.03-T02 Create Imaris surfaces with a volume filter and export statistics
Original instruction
Open input/gfp_cells.ims in Imaris. Create Surfaces on the GFP channel with 0.5 µm smoothing, background subtraction, a threshold you set by inspecting the overlay, split touching objects by seed points, and filter to volume >10 µm³. Export statistics to output/surfaces.csv and save output/scene.ims.
- Platforms
win· Windowsmac· macOS- Applications
- Imaris
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgment- Work product
WP10· Annotations- Conditions
licensed· Licensed pro app- Proposed difficulty
- 3 / 5
Proposed verifier
Object count and mean volume within 5% of the reference analysis; all retained objects >10 µm³; the saved scene must contain the Surfaces object with the smoothing and split settings (Imaris XT/Python is disabled).
Proposed partial credit
25% surface creation; 20% splitting; 30% count and volumes; 25% filter and export.
R08.07.01.03-T03 Track 30 frames in TrackMate and fix two identity swaps
Original instruction
Open input/mitosis_30f.tif in Fiji and run TrackMate: LoG detector (estimated diameter 8 µm, threshold tuned on the preview), LAP tracker with linking 10 µm, gap-closing 12 µm over 2 frames. Then fix the two identity swaps listed in input/notes.txt in the TrackScheme editor and export output/tracks.xml.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- Fiji/ImageJ · TrackMate
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgmentav· Audio/video over time- Work product
WP10· Annotations- Conditions
- None declared
- Proposed difficulty
- 4 / 5
Proposed verifier
TRA score ≥0.9 against the hidden ground truth; the two swapped track pairs must be correctly reassigned (checked per-frame labels at the swap frames); track count within ±2 of gold. Fiji's macro runner, Script Editor and --headless mode are disabled, so TrackMate must be driven from its GUI and TrackScheme.
Proposed partial credit
35% detection and linking quality; 40% two swaps fixed; 25% TRA threshold.
R08.07.01.03-T04 Complete neuron trajectories in a 4D recording preserving identity
Original instruction
Open input/137.h5 in the napari-based POINTS annotation GUI with the partial annotation input/points_partial.csv: positions exist for t=1 only. Propagate and correct the 30 neuron positions through t=1..30, keeping identities consistent across frames, and export output/points.csv with columns t, id, x, y, z.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- napari · POINTS
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
drag· Drag & dropclick· Point & clickvis· Visual judgmentnav· Pan/zoom/scroll- Work product
WP10· Annotations- Conditions
long· Long-horizon- Proposed difficulty
- 5 / 5
Proposed verifier
Per-frame position error ≤3 voxels for ≥90% of neuron-frames and identity accuracy ≥0.9 against the hidden annotation; CSV must keep the given id contract (same ids as t=1). napari's IPython console is disabled and the agent has no Python shell outside the napari GUI.
Proposed partial credit
30% positions accurate; 45% identities preserved; 15% full 30 frames covered; 10% format contract.
R08.07.01.03-T05 Curate TrackMate tracks: remove spurious short tracks and merge split ones
Original instruction
Open input/tracks_raw.xml with input/movie.tif in Fiji's TrackMate. In TrackScheme delete tracks shorter than 5 frames that sit on debris, and reconnect the 4 tracks that were split by missed detections (gaps of 1–2 frames) by adding links. Export output/tracks_curated.xml and output/summary.csv (track count, mean duration).
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- Fiji/ImageJ · TrackMate
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgmentnav· Pan/zoom/scroll- Work product
WP10· Annotations- Conditions
- None declared
- Proposed difficulty
- 4 / 5
Proposed verifier
Debris tracks removed (none of the gold debris ids remain) and the 4 reconnections present as single tracks spanning both segments; TRA ≥0.92; real short tracks (mitotic daughters) must be kept. Fiji's macro runner, Script Editor and --headless mode are disabled, so TrackMate must be driven from its GUI and TrackScheme.
Proposed partial credit
30% debris removed; 40% four merges; 20% real short tracks kept; 10% summary.
R08.07.01.03-T06 Build an Imaris animation flying through a volume with a clipping plane
Original instruction
Open input/organoid.ims in Imaris. Make a 10 s, 25 fps, 1920×1080 animation that starts on a whole-volume view, rotates 180° about the vertical axis, then advances a clipping plane through the organoid to reveal the lumen, with a scale bar visible throughout. Export output/flythrough.mp4 and save output/scene.ims.
- Platforms
win· Windowsmac· macOS- Applications
- Imaris
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
drag· Drag & dropclick· Point & clickvis· Visual judgmentav· Audio/video over time- Work product
WP05· Time-based media- Conditions
licensed· Licensed pro app- Proposed difficulty
- 4 / 5
Proposed verifier
ffprobe: 250 frames, 1920×1080. Frame checks: rotation completes 180±10° (feature-matching on frames 0 and 125), clipping plane advances monotonically in the second half (visible cross-section area grows), scale bar present in every sampled frame. Imaris XT (Python/MATLAB extensions) is disabled and h5py is absent from the VM.
Proposed partial credit
20% format; 30% rotation; 35% clipping sweep; 15% scale bar and scene saved.
R08.07.01.03-T07 Measure a 3D distance between two labelled structures in napari
Original instruction
Open input/dual_label.tif in napari (two channels). Using a Points layer, mark the centre of the labelled centrosome and the centre of the nearest nuclear envelope indentation in 3D, then write the Euclidean distance in µm (voxel size in input/meta.json) to output/answer.json and save output/points.csv.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- napari
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clicknav· Pan/zoom/scrollvis· Visual judgmentgeom· Precise geometry- Work product
WP12· Answer/decision- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
Each point within 4 voxels of the gold location in 3D and the distance within 8% of gold with anisotropic scaling applied (ignoring z spacing gives a detectable error). napari's IPython console is disabled and the agent has no Python shell outside the napari GUI.
Proposed partial credit
35% centrosome point; 35% envelope point; 30% distance with correct scaling.
R08.07.01.03-T08 Set up an Imaris Spots tracking run and export track statistics
Original instruction
Open input/beads_4d.ims in Imaris. Detect Spots on channel 1 (estimated diameter 1.5 µm, background subtraction, quality filter set from the histogram), track with Autoregressive Motion (max distance 4 µm, max gap 2), and export track displacement, speed and straightness to output/track_stats.csv. Save output/scene.ims.
- Platforms
win· Windowsmac· macOS- Applications
- Imaris
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgment- Work product
WP10· Annotations- Conditions
licensed· Licensed pro app- Proposed difficulty
- 3 / 5
Proposed verifier
Spot count per frame within 8% of reference; track count within 10%; mean speed and straightness within 10% of the reference analysis with the same parameters. Imaris XT (Python/MATLAB extensions) is disabled and h5py is absent from the VM.
Proposed partial credit
30% spot detection; 25% tracking parameters; 35% statistics; 10% export and scene.
R08.07.01.03-T09 Build a lineage tree through two divisions in TrackMate
Original instruction
Open input/divisions.tif in Fiji TrackMate and track the single founder cell through two rounds of division (frames 1–40), allowing track splitting. In TrackScheme verify the branch structure, correct one wrongly assigned daughter, and export output/lineage.xml plus output/lineage.csv (parent id, daughter ids, division frames).
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- Fiji/ImageJ · TrackMate
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgmentav· Audio/video over time- Work product
WP10· Annotations- Conditions
long· Long-horizon- Proposed difficulty
- 5 / 5
Proposed verifier
Lineage topology must be isomorphic to gold (one founder, two generations, 4 leaves); division frames within ±1; the corrected daughter assignment matches gold; TRA ≥0.9. Fiji's macro runner, Script Editor and --headless mode are disabled, so TrackMate must be driven from its GUI and TrackScheme.
Proposed partial credit
35% topology; 25% division frames; 25% daughter correction; 15% exports.
R08.07.01.03-T10 Render an orthogonal three-view figure of a volume in napari
Original instruction
Open input/stack.tif in napari and produce a single figure image output/ortho.png containing XY, XZ and YZ views through the voxel given in input/point.json, each with a 10 µm scale bar and identical contrast limits. Save output/view_state.json describing the slice positions.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- napari
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicknav· Pan/zoom/scrollvis· Visual judgment- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
Three panels detected; each panel's slice must pass within 2 voxels of the given point (image correlation against reference slices ≥0.95); scale bars present with correct length in pixels for each view's aspect; contrast limits equal across panels; view_state.json slice indices must match the panels detected in the image. napari's IPython console is disabled and the agent has no Python shell outside the napari GUI.
Proposed partial credit
40% three correct slices; 25% scale bars; 20% matched contrast; 15% state file.
R08.07.01.03-T11 Spot and fix tracking failures caused by a z-drift in a long movie
Original instruction
input/longmovie.tif (120 frames) drifts in z from frame 60, so tracks in input/tracks.xml break there. In Fiji inspect the drift, apply a z-drift correction, re-run TrackMate with the same parameters, and export output/tracks_fixed.xml plus the drift profile output/drift.csv.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- Fiji/ImageJ · TrackMate
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
vis· Visual judgmentnav· Pan/zoom/scrollclick· Point & clickav· Audio/video over time- Work product
WP10· Annotations- Conditions
long· Long-horizonhidden· Hidden/stale state- Proposed difficulty
- 5 / 5
Proposed verifier
Drift profile within 1 slice of gold per frame; after correction, track fragmentation at frames 58–65 drops to the pre-drift rate and TRA ≥0.88 against ground truth.
Proposed partial credit
30% drift measured; 35% correction applied; 25% tracking recovers; 10% exports.
R08.07.01.03-T12 Create an Imaris surface-to-surface distance analysis and report contacts
Original instruction
Open input/two_structures.ims in Imaris. Build Surfaces for both channels, compute the shortest distance from channel-2 surfaces to channel-1 surfaces, filter channel-2 objects within 0.5 µm, and report their count and total volume in output/answer.json. Export statistics to output/distances.csv.
- Platforms
win· Windowsmac· macOS- Applications
- Imaris
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
AP· API-sufficient- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgment- Work product
WP10· Annotations- Conditions
licensed· Licensed pro app- Proposed difficulty
- 3 / 5
Proposed verifier
Count and total volume within 8% of the reference analysis; distances.csv must hold a shortest-distance column consistent with the filter; both Surfaces objects present in the saved scene. Imaris XT (Python/MATLAB extensions) is disabled and h5py is absent from the VM.
Proposed partial credit
30% both surfaces; 25% distance measure; 35% filtered count and volume; 10% export.
R08.07.01.03-T13 Set clipping planes and channel blending for a dual-label volume in napari
Original instruction
Open input/dual_channel.tif in napari. Show channel 1 in green additive blending at 50% opacity and channel 2 in magenta, clip the volume so only the top 30% of z is rendered, and save output/clipped.png plus output/layers.json listing the layer settings.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- napari
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgment- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
layers.json must report the stated colormaps, blending and opacity, and re-rendering with them must reproduce clipped.png (SSIM ≥0.95); no signal from the lower 70% of z (correlation with the bottom-slab projection <0.2); SSIM ≥0.85 vs the reference render. napari's IPython console is disabled and the agent has no Python shell outside the napari GUI.
Proposed partial credit
35% channel settings; 40% clipping correct; 25% render matches.
R08.07.01.03-T14 Measure instantaneous migration speed from curated tracks
Original instruction
Open input/tracks_curated.xml with input/movie.tif in Fiji TrackMate, compute per-track mean speed and the population median in µm/min (frame interval in input/meta.json), and write output/speeds.csv and output/answer.json. Exclude tracks shorter than 10 frames.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- Fiji/ImageJ · TrackMate
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clickvis· Visual judgment- Work product
WP02· Records/table- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
Per-track speeds within 5% of reference with correct time and space calibration; median within 5%; only tracks ≥10 frames included (count matches gold).
Proposed partial credit
30% calibration correct; 40% per-track speeds; 20% median; 10% filtering.
R08.07.01.03-T15 Check 4D registration visually and fix a misaligned timepoint
Original instruction
Open input/timelapse_registered.tif in napari and scrub through time: one timepoint is misregistered by a visible xy shift. Identify it, estimate the shift in pixels, correct that frame in Fiji, and save output/fixed.tif plus output/answer.json (frame index, dx, dy).
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- napari · Fiji/ImageJ
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
nav· Pan/zoom/scrollvis· Visual judgmentav· Audio/video over timemulti· Cross-app- Work product
WP10· Annotations- Conditions
multiapp· Multi-apphidden· Hidden/stale state- Proposed difficulty
- 3 / 5
Proposed verifier
Frame index exact; dx and dy within 2 px of gold; after correction, frame-to-frame cross-correlation at that transition rises above 0.95 and other frames are unchanged (checksum). napari's IPython console and Fiji's macro runner/Script Editor are disabled, and the agent has no Python shell.
Proposed partial credit
35% frame identified; 35% shift estimated; 20% corrected file; 10% others unchanged.
R08.07.01.03-T16 Control: run TrackMate headless and compute track statistics by script
Original instruction
Control pair of T03. Run TrackMate from a headless Fiji script (or trackpy) on input/mitosis_30f.tif with the same detector and tracker settings, apply the swap corrections listed in input/notes.txt programmatically, and export output/tracks.xml.
- Platforms
lin· Linuxmac· macOS- Applications
- Fiji/ImageJ · TrackMate
- Interfaces
term· Terminal- GUI need · task setting
CL· CLI-sufficient- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
code· Code & commands- Work product
WP10· Annotations- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
Same checker as T03 (TRA ≥0.9, both swaps corrected, track count within ±2). Scored as the CLI control of T03.
Proposed partial credit
40% tracking quality; 40% swaps corrected; 20% export valid.
R08.07.01.03-T17 Build an Imaris Filament tracing of a neuron and report branch metrics
Original instruction
Open input/neuron_3d.ims in Imaris and trace the neuron with FilamentTracer (autopath from a seed you place at the soma), correct false branches by inspection, and export total dendrite length, branch count and maximum branch order to output/answer.json with statistics in output/filaments.csv. Save output/scene.ims.
- Platforms
win· Windowsmac· macOS- Applications
- Imaris
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
drag· Drag & dropclick· Point & clickvis· Visual judgmentnav· Pan/zoom/scroll- Work product
WP10· Annotations- Conditions
licensed· Licensed pro applong· Long-horizon- Proposed difficulty
- 5 / 5
Proposed verifier
Total length within 10%, branch count within 15% and max branch order exact versus the expert tracing; the saved scene must contain a Filament object with a soma seed point. Imaris XT (Python/MATLAB extensions) is disabled and h5py is absent from the VM.
Proposed partial credit
25% tracing created; 30% total length; 25% branch count; 20% branch order.
R08.07.01.03-T18 Animate a timelapse with a time stamp and track overlays in napari
Original instruction
Open input/timelapse.tif and input/tracks.csv in napari. Add a Tracks layer with 10-frame tails, a time stamp text overlay in minutes (interval in input/meta.json), and export a 1280×720, 15 fps movie of all 60 frames to output/movie.mp4.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- napari
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgmentav· Audio/video over time- Work product
WP05· Time-based media- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
ffprobe: 60 frames, 1280×720, 15 fps. OCR of sampled frames gives time stamps matching frame × interval within 0.1 min; track tails visible (overlay pixel count >0 in ≥55 frames) and tail length consistent with 10 frames.
Proposed partial credit
25% movie format; 30% time stamps; 30% track overlay; 15% all frames included.
R08.07.01.03-T19 Separate dividing from non-dividing cells by curating tracks in Imaris
Original instruction
Open input/dividing_cells.ims in Imaris. Track Spots over 50 frames, enable track splitting, then curate the lineages so every true division is a split and the 3 false splits (crossing cells) are removed. Export output/lineages.csv (track id, division frames) and report the number of dividing cells in output/answer.json.
- Platforms
win· Windowsmac· macOS- Applications
- Imaris
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgmentav· Audio/video over time- Work product
WP10· Annotations- Conditions
licensed· Licensed pro applong· Long-horizon- Proposed difficulty
- 4 / 5
Proposed verifier
Dividing-cell count exact versus expert annotation; division frames within ±2 for ≥90% of events; none of the 3 crossing events reported as divisions. Imaris XT (Python/MATLAB extensions) is disabled and h5py is absent from the VM.
Proposed partial credit
25% tracking with splits; 35% division count; 25% false splits removed; 15% frames accurate.
R08.07.01.03-T20 Produce a publication movie panel from a 4D dataset across two apps
Original instruction
From input/embryo_4d.tif build a two-panel movie: left, a napari MIP with a 20 µm scale bar; right, the same volume with segmentation labels from input/labels.tif at 40% opacity. Render both at 960×720, 10 fps, 100 frames, combine them side by side in Fiji (or ffmpeg) with a shared time stamp, and save output/panel.mp4.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- napari · Fiji/ImageJ
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clickvis· Visual judgmentav· Audio/video over timemulti· Cross-app- Work product
WP05· Time-based media- Conditions
multiapp· Multi-applong· Long-horizon- Proposed difficulty
- 4 / 5
Proposed verifier
ffprobe: 1920×720, 100 frames, 10 fps. Left half matches the reference MIP frames (SSIM ≥0.85), right half shows label overlay (colour-variance test) at the same frame index; time stamp identical across panels; scale bar present.
Proposed partial credit
25% left panel; 25% right panel; 25% synchronized combination; 25% annotations and format.
Mapped research references
Existing benchmark-to-class links from the research catalog. They are not record-level annotations, executions or product endorsements.