ROI drawing & manual measurement
Draw regions and measure intensity, area and counts.
20 project-authored proposals · taxonomy v1.1 · 0 new benchmark runs. Verifiers and partial-credit rules below are designs, not executed results.
- Typical applications
- Fiji/ImageJ · QuPath · napari
- Class GUI-need label
G3· GUI-only
Task proposals · 20
Expand to inspect the complete original wording and proposed checks. Original proposal text remains English in both interfaces.
R08.07.01.01-T01 Outline six arrow-marked nuclei in Fiji and measure area and channel-2 mean
Original instruction
Open input/nuclei_2ch.tif in Fiji. input/arrows.png marks six nuclei with yellow arrows. Outline exactly those six with the freehand or wand tool, add each to the ROI Manager in the arrow order, measure Area and Mean of channel 2, and save output/RoiSet.zip and output/Results.csv.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- Fiji/ImageJ
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
path· Continuous pathclick· Point & clickvis· Visual judgment- Work product
WP10· Annotations- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
Six ROIs, each IoU ≥0.7 with the matching hidden mask and in the arrow order; Area and channel-2 Mean within 5% of the mask values. Masks and arrow coordinates are not in the workspace; macro-driven global thresholding cannot select only these six (other nuclei share intensity). Fiji's macro runner, Script Editor and --headless mode are disabled, and a file-system audit flags ROI or results files not written by Fiji.
Proposed partial credit
60% six ROIs with IoU ≥0.7 (10 pts each); 25% measurements; 15% order and files.
R08.07.01.01-T02 Trace a neurite with a segmented line in Fiji and report calibrated length
Original instruction
Open input/neuron.tif in Fiji (pixel size in metadata). Using the segmented-line tool, trace the neurite from the soma at the coordinates in input/note.txt to its distal tip, add the ROI to the ROI Manager, and write the calibrated length in µm to output/answer.json. Save output/RoiSet.zip.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- Fiji/ImageJ
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
path· Continuous pathclick· Point & clickvis· Visual judgmentnav· Pan/zoom/scroll- Work product
WP10· Annotations- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
Length within 3% of the gold tracing; the saved ROI's polyline must stay within 3 px of the gold centerline for ≥90% of its length (so a straight line between endpoints fails). Fiji's macro runner, Script Editor and --headless mode are disabled, and a file-system audit flags ROI or results files not written by Fiji.
Proposed partial credit
50% length within the 3-percent band; 40% path follows the neurite; 10% ROI saved.
R08.07.01.01-T03 Mark every dividing cell in one frame with a napari Points layer
Original instruction
Open input/mitosis.tif in napari and go to frame 12. Add a Points layer named 'mitotic' and click once on each cell in mitosis (condensed chromatin, rounded morphology), then export the points to output/points.csv with columns axis-0, axis-1 (frame excluded).
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- napari
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickvis· Visual judgmentnav· Pan/zoom/scroll- Work product
WP10· Annotations- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
F1 ≥0.8 against the hidden annotation at a 5-px match radius; points must lie inside the matched cell masks. Frame 12 contains 9 mitotic cells among ~180 interphase cells of similar intensity. napari's IPython console is disabled, the agent has no Python shell, and a file-system audit flags layer files not written by the napari process.
Proposed partial credit
70% F1 (full ≥0.8, zero ≤0.4); 20% all points inside cells; 10% export format.
R08.07.01.01-T04 Repair a broken ROI set in Fiji and run Multi Measure
Original instruction
Open input/stack.tif in Fiji and load input/RoiSet_bad.zip: two ROIs are associated with the wrong z-slice and one is a duplicate. Move the two to the slices where their objects actually are, delete the duplicate, run Multi Measure (Area, Mean, Min, Max per slice), and save output/RoiSet_fixed.zip and output/Results.csv.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- Fiji/ImageJ
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickvis· Visual judgmentnav· Pan/zoom/scroll- Work product
WP10· Annotations- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
Fixed set has n−1 ROIs with slice positions equal to gold and geometries unchanged (IoU ≥0.95 with the input ROIs); Results.csv rows and values match the gold Multi Measure table within 1%. Fiji's macro runner, Script Editor and --headless mode are disabled, and a file-system audit flags ROI or results files not written by Fiji.
Proposed partial credit
40% slice assignments; 20% duplicate removed; 30% measurement table; 10% geometries preserved.
R08.07.01.01-T05 Outline a germinal center in QuPath and export a classified GeoJSON
Original instruction
Open input/lymph_node.ome.tif in QuPath. input/ref.png shows the germinal center to annotate. Draw it as a polygon annotation, set its classification to 'Region*', then export annotations to output/annotations.geojson.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- QuPath
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
path· Continuous pathclick· Point & clickvis· Visual judgmentnav· Pan/zoom/scroll- Work product
WP10· Annotations- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
One polygon with IoU ≥0.6 against the hidden expert mask and classification exactly 'Region*'. The slide contains three germinal centers; only the one shown in ref.png counts, so automated detection of all three fails. QuPath's script editor and command-line script mode are disabled, and a file-system audit flags exports not written by QuPath.
Proposed partial credit
60% correct region (IoU scaled); 25% classification; 15% GeoJSON export valid.
R08.07.01.01-T06 Measure a line profile across a cell junction in Fiji and report FWHM
Original instruction
Open input/junction.tif in Fiji. Draw a 10-px-wide straight line perpendicular to the junction at the position marked in input/mark.png, get the intensity profile, fit a Gaussian, and write the FWHM in µm and the peak intensity to output/answer.json. Save the line ROI to output/RoiSet.zip.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- Fiji/ImageJ
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
path· Continuous pathclick· Point & clickvis· Visual judgment- Work product
WP10· Annotations- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
Line must cross the junction within 5 px of the marked position and be within 10° of perpendicular; FWHM within 8% and peak within 5% of gold. Fiji's macro runner, Script Editor and --headless mode are disabled, and a file-system audit flags ROI or results files not written by Fiji.
Proposed partial credit
30% line placement and angle; 45% FWHM; 25% peak intensity.
R08.07.01.01-T07 Measure nuclear-to-cytoplasmic ratio with paired ROIs in Fiji
Original instruction
Open input/translocation.tif in Fiji (ch1 DAPI, ch2 transcription factor). For the 10 cells numbered in input/cells.png, draw a nuclear ROI and a cytoplasmic ring ROI for each, measure ch2 means, and save output/RoiSet.zip plus output/ratios.csv with cell id, nuclear mean, cytoplasmic mean and N/C ratio.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- Fiji/ImageJ
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
path· Continuous pathclick· Point & clickvis· Visual judgment- Work product
WP10· Annotations- Conditions
long· Long-horizon- Proposed difficulty
- 4 / 5
Proposed verifier
Per cell: nuclear ROI IoU ≥0.7 with the hidden nuclear mask, cytoplasmic ROI ≥70% inside the hidden cytoplasm mask and ≤5% overlapping the nucleus; N/C ratios within 10% of gold for ≥8 of 10 cells. Fiji's macro runner, Script Editor and --headless mode are disabled, and a file-system audit flags ROI or results files not written by Fiji.
Proposed partial credit
35% nuclear ROIs; 35% cytoplasmic rings; 30% ratios.
R08.07.01.01-T08 Count and measure red yeast colonies on an agar plate image in Fiji
Original instruction
Open input/agar.png in Fiji. Count only the red colonies (white colonies and plate artifacts must be excluded) by setting an appropriate colour/channel approach and correcting merges by hand, then export output/colonies.csv with centroid x, y and area per colony and the total in output/answer.json.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- Fiji/ImageJ
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickpath· Continuous pathvis· Visual judgment- Work product
WP10· Annotations- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
Count within the hidden band (±5% of 212); centroid F1 ≥0.9 at a 10-px radius; no white colony among reported centroids (checked against the hidden white-colony mask). Fiji's macro runner, Script Editor and --headless mode are disabled, and a file-system audit flags ROI or results files not written by Fiji.
Proposed partial credit
35% count in band; 35% centroid F1; 20% no white colonies; 10% area column present.
R08.07.01.01-T09 Measure organelle contacts in 3D with napari shapes and labels
Original instruction
Open input/organelles.tif (3-channel, 40 z-slices) in napari. For the 5 cells listed in input/cells.txt, draw a Labels annotation of the mitochondrial network in the single slice of best focus per cell and a Points layer on each ER–mitochondria contact you can see. Save output/labels.tif and output/contacts.csv.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- napari
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
path· Continuous pathclick· Point & clickvis· Visual judgmentnav· Pan/zoom/scroll- Work product
WP10· Annotations- Conditions
long· Long-horizon- Proposed difficulty
- 5 / 5
Proposed verifier
Per cell: label mask IoU ≥0.6 with the expert mask on the chosen slice (slice must be within ±2 of the gold best-focus slice); contact points F1 ≥0.7 at 4 px. napari's IPython console is disabled, the agent has no Python shell, and a file-system audit flags layer files not written by the napari process.
Proposed partial credit
25% correct focus slices; 40% mitochondrial masks; 35% contact points.
R08.07.01.01-T10 Draw a wand-based ROI on one cell and subtract local background in Fiji
Original instruction
Open input/single_cell.tif in Fiji. Use the wand tool with a tolerance you choose to select the cell body, then draw a nearby background ROI of similar size in an empty region. Measure both means, write the background-subtracted cell mean and the ROI areas to output/answer.json, and save output/RoiSet.zip.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- Fiji/ImageJ
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickvis· Visual judgment- Work product
WP10· Annotations- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
Cell ROI IoU ≥0.8 with the hidden mask; background ROI must not overlap any cell mask and be within 50–200% of the cell area; subtracted mean within 5% of gold. Fiji's macro runner, Script Editor and --headless mode are disabled, and a file-system audit flags ROI or results files not written by Fiji.
Proposed partial credit
40% cell ROI; 25% valid background ROI; 35% subtracted value.
R08.07.01.01-T11 Count Ki-67 positive tumour nuclei in a QuPath annotation and report the index
Original instruction
Open input/ki67_slide.ome.tif in QuPath. Draw a 1 mm² tumour-region annotation inside the area indicated in input/region_hint.png, run cell detection, classify nuclei as Ki-67 positive or negative using a threshold you tune by eye, and report positive count, total and index in output/answer.json. Save the project.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- QuPath
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
path· Continuous pathclick· Point & clickvis· Visual judgmentnav· Pan/zoom/scroll- Work product
WP10· Annotations- Conditions
- None declared
- Proposed difficulty
- 4 / 5
Proposed verifier
Annotation area 1.0±0.1 mm² inside the hinted region; Ki-67 index within 5 percentage points of the expert count for the same region; total detected nuclei within 15% of reference. QuPath's script editor and command-line script mode are disabled, and a file-system audit flags exports not written by QuPath.
Proposed partial credit
25% region drawn; 25% detection; 40% index; 10% project saved.
R08.07.01.01-T12 Measure three angles between cell-division axes in Fiji
Original instruction
Open input/divisions.tif in Fiji. For the three dividing cells circled in input/circles.png, use the angle tool to measure the angle between the division axis (spindle poles) and the tissue axis drawn in input/tissue_axis.png, and save output/angles.csv with cell id and angle in degrees plus output/RoiSet.zip.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- Fiji/ImageJ
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickgeom· Precise geometryvis· Visual judgment- Work product
WP10· Annotations- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
Each angle within 5° of gold; angle ROIs' vertices must sit within 8 px of the gold spindle poles and tissue-axis direction. Fiji's macro runner, Script Editor and --headless mode are disabled, and a file-system audit flags ROI or results files not written by Fiji.
Proposed partial credit
90% angles within 5° (30 pts each); 10% ROI geometry saved.
R08.07.01.01-T13 Measure a wound-closure area over three timepoints in Fiji
Original instruction
Open input/scratch_assay.tif (3 timepoints) in Fiji. For each timepoint, outline the cell-free wound area with the polygon or freehand tool, measure the area in mm², and write output/wound.csv (timepoint, area, percent closure vs t0). Save output/RoiSet.zip with one ROI per timepoint.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- Fiji/ImageJ
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
path· Continuous pathclick· Point & clickvis· Visual judgment- Work product
WP10· Annotations- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
Per-timepoint ROI IoU ≥0.85 with expert masks and areas within 8%; percent closure consistent with the reported areas. Phase-contrast texture defeats global thresholding (reference macro attempt gives IoU 0.5). Fiji's macro runner, Script Editor and --headless mode are disabled, and a file-system audit flags ROI or results files not written by Fiji.
Proposed partial credit
60% three ROIs (20 pts each); 25% areas; 15% closure column.
R08.07.01.01-T14 Edit an auto-segmentation in napari: split merges and remove debris
Original instruction
Open input/cells.tif and the auto labels input/labels_auto.tif in napari. Using the paintbrush and fill tools, split the 6 merged label pairs and delete the 11 debris labels listed in input/qc_notes.txt, keeping all other labels unchanged, and save output/labels_fixed.tif.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- napari
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
path· Continuous pathclick· Point & clickvis· Visual judgmentnav· Pan/zoom/scroll- Work product
WP10· Annotations- Conditions
long· Long-horizon- Proposed difficulty
- 4 / 5
Proposed verifier
After matching, split pairs must each yield two labels with IoU ≥0.7 to the gold cells; all 11 debris labels absent; untouched labels byte-identical to the input (allowing id renumbering). napari's IPython console is disabled, the agent has no Python shell, and a file-system audit flags layer files not written by the napari process.
Proposed partial credit
45% merges split (7.5 pts each); 30% debris removed; 25% other labels unchanged.
R08.07.01.01-T15 Measure colocalization inside hand-drawn ROIs in Fiji
Original instruction
Open input/coloc.tif in Fiji (ch1 green, ch2 red). Draw ROIs around the 8 cells marked in input/marks.png, and for each compute Pearson's r and Manders' M1/M2 with Coloc 2 using the ROI as the mask, writing output/coloc.csv. Save output/RoiSet.zip.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- Fiji/ImageJ · Coloc 2
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
path· Continuous pathclick· Point & clickvis· Visual judgment- Work product
WP10· Annotations- Conditions
- None declared
- Proposed difficulty
- 4 / 5
Proposed verifier
Per cell: ROI IoU ≥0.75 to the hidden mask; Pearson's r within 0.05 and Manders within 0.07 of gold values computed in the gold ROIs for ≥7 of 8 cells. Fiji's macro runner, Script Editor and --headless mode are disabled, and a file-system audit flags ROI or results files not written by Fiji.
Proposed partial credit
40% ROIs; 40% coefficients; 20% complete table.
R08.07.01.01-T16 Count immunopositive cells in three cortical layers of a brain section
Original instruction
Open input/brain_section.ome.tif in QuPath. Draw boundaries for cortical layers II/III, IV and V following the cytoarchitecture (layer hints in input/layers_ref.png), run positive-cell detection for the DAB channel inside each, and report counts and densities per mm² in output/layers.csv. Save the project.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- QuPath
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
path· Continuous pathclick· Point & clickvis· Visual judgmentnav· Pan/zoom/scroll- Work product
WP10· Annotations- Conditions
long· Long-horizon- Proposed difficulty
- 5 / 5
Proposed verifier
Each layer annotation IoU ≥0.7 with the expert boundary; positive counts within 15% and densities within 15% of the expert values per layer. No layer annotation file exists in the inputs. QuPath's script editor and command-line script mode are disabled, and a file-system audit flags exports not written by QuPath.
Proposed partial credit
45% three layer boundaries (15 pts each); 35% counts; 20% densities.
R08.07.01.01-T17 Control: segment the arrow-marked nuclei by script using the given coordinates
Original instruction
Control pair of T01. With input/arrow_coords.csv (the six arrow tip coordinates) provided, use scikit-image or an ImageJ headless macro from the terminal to segment the six nuclei containing those points, measure Area and channel-2 Mean, and write output/Results.csv and output/masks.tif.
- Platforms
lin· Linuxmac· macOS- Applications
- scikit-image · Fiji/ImageJ
- 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
- 2 / 5
Proposed verifier
Same tolerances as T01 (per-nucleus IoU ≥0.7, measurements within 5%). Scored as the CLI control of T01; the coordinates are given here precisely because the GUI version must find them visually.
Proposed partial credit
60% six masks; 30% measurements; 10% output format.
R08.07.01.01-T18 Measure a cell-size histogram from hand-drawn ROIs and report the median
Original instruction
Open input/tissue.tif in Fiji and outline 30 cells sampled across the field (at least 5 per quadrant) with the freehand tool. Measure Area and Feret diameter, save output/RoiSet.zip and output/sizes.csv, and report the median Feret diameter in µm in output/answer.json.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- Fiji/ImageJ
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
path· Continuous pathclick· Point & clickvis· Visual judgment- Work product
WP10· Annotations- Conditions
long· Long-horizon- Proposed difficulty
- 4 / 5
Proposed verifier
30 ROIs, each matching a distinct hidden cell mask with IoU ≥0.7, ≥5 per image quadrant; median Feret within 8% of the population median from the full hidden annotation. Fiji's macro runner, Script Editor and --headless mode are disabled, and a file-system audit flags ROI or results files not written by Fiji.
Proposed partial credit
40% 30 valid ROIs (scaled); 20% quadrant spread; 30% median; 10% files.
R08.07.01.01-T19 Measure sarcomere spacing from an intensity profile in Fiji
Original instruction
Open input/myofibril.tif in Fiji. Draw a line along a single myofibril through at least 10 sarcomeres, take the plot profile, and from peak positions report mean sarcomere length in µm and its standard deviation in output/answer.json. Save output/RoiSet.zip and output/profile.csv.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- Fiji/ImageJ
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
path· Continuous pathclick· Point & clickvis· Visual judgmentnav· Pan/zoom/scroll- Work product
WP10· Annotations- Conditions
- None declared
- Proposed difficulty
- 4 / 5
Proposed verifier
Line must stay within 4 px of the gold myofibril axis over ≥90% of its length and span ≥10 sarcomeres; mean spacing within 5% and SD within 25% of gold. Fiji's macro runner, Script Editor and --headless mode are disabled, and a file-system audit flags ROI or results files not written by Fiji.
Proposed partial credit
35% line placement and span; 45% mean spacing; 20% SD and profile export.
R08.07.01.01-T20 Build a composite ROI of only the infiltrated stroma in QuPath
Original instruction
Open input/tumor_slide.ome.tif in QuPath. Annotate the stromal region that is infiltrated by lymphocytes (dense small dark nuclei) as a single annotation, excluding tumour nests and empty space by using annotation subtraction, classify it 'Stroma', and export output/stroma.geojson plus its area in mm² in output/answer.json.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- QuPath
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
path· Continuous pathclick· Point & clickvis· Visual judgmentnav· Pan/zoom/scroll- Work product
WP10· Annotations- Conditions
long· Long-horizon- Proposed difficulty
- 5 / 5
Proposed verifier
IoU ≥0.6 with the expert mask; overlap with tumour-nest masks <5% of the annotation area; classification 'Stroma'; area within 10% of expert value. QuPath's script editor and command-line script mode are disabled, and a file-system audit flags exports not written by QuPath.
Proposed partial credit
50% IoU; 25% tumour exclusion; 15% area; 10% class and export.
Mapped research references
Existing benchmark-to-class links from the research catalog. They are not record-level annotations, executions or product endorsements.