From scans to figures, signal plots, and survival curves

1. Import and check scans

1. Choose + New experiment and name it “Two-group example”. Use Import or drag acquisition folders into the app.
2. Keep each folder’s ClickInfo.txt and luminescent.TIF together. Include photograph.TIF if available. You can import a parent folder containing multiple acquisitions.
3. In Scans, check each acquisition date and time-point assignment. Both September 1 cages should belong to the same time point; repeat for September 8 and 15.

Standalone TIFF, PNG, and JPEG files are rendered-only panels. They cannot recover quantitative radiance or provide calibrated ROI measurements. Project files with .amix or .aurax extensions are not opened; unzip acquisition folders before importing.

Normalized radiance compares previews on a shared scale. Turn it off to inspect a dim scan using its own range. Colors then cannot be compared between scans. This preview setting affects the radiance layer only; it leaves the photograph, figure scale, plots, and measurements unchanged. Set aside saturated exposures when a suitable unsaturated acquisition is available.

2. Identify animals and groups

1. Open the crop tool from a scan. For a large experiment, choose Auto-detect mice to propose outlines from the photograph. Accept or dismiss each proposal, reshape an accepted outline when needed, and assign the animal’s name. You can also draw a rectangle or freehand mouse outline manually. Use C1/C2 in the control cage and T1/T2 in the treatment cage.
2. On later dates, assign the same animal identities. A new name creates a different animal rather than a follow-up measurement.
3. Selections save automatically as you draw and edit. Use Previous cage and Next cage to continue; check the save status before leaving.
4. Create Control and Treatment groups and assign animals. In Figure, use Groups & treatments; in other views, use the Groups sidebar.

You can also use Animals → + Add to generate numbered names or paste a spreadsheet column such as:

C1
C2
T1
T2

Review proposed boundaries, separate touching animals, and confirm identities on every scan. A suggested outline is not a validated measurement region.

3. Build a shared-scale figure

1. Select Figure and Panel view → Individual animals. With all example assignments complete, expect four animals across three time points: 12 panels.
2. Choose Mouse order → Group to keep treatments together. Use Mouse name or Custom order when appropriate. Remove side padding fits panels to their crops.
3. Click Normalize all. Check the shared color bar. Advanced exposes manual min/max, log/linear mapping, and colormap controls.
4. For cage-level presentation, switch to Whole scans. Choose animal outlines or a group-composition strip; review the cage label.
5. Review labels, missing panels, crops, and any pre-export issues. Choose Export figure for the displayed figure as a 300 dpi PNG.

4. Plot signal and export measurements

1. Open Plot → Signal over time. Choose Lines → Individual animals and a metric: Total flux, Mean radiance, or Max radiance. Hover an individual line to see which animal it represents.
2. Choose Name, Date, or Day # labels. For this example, use Day # and First image = Day 0; the three dates are days 0, 7, and 14.
3. Switch to Group summary for Mean or Median with Standard deviation or Standard error. Check visible groups and the selected summary before export. Use Linear Y to inspect zero values, which cannot be displayed on a logarithmic axis.
4. Download CSV for data, SVG (vector) for an editable plot, or Export plot for a 300 dpi PNG. Plot image exports include the group legend.

Without an explicit measurement ROI, signal plots use the animal’s crop rectangle or freehand contour. An explicit ROI is separate from the crop and decorative panel border. Keep region selection consistent across dates. Advanced ROI controls expose measurements and a project-wide ROI CSV export; dashed measurement overlays are omitted from exported figures.

Total flux is an estimate calculated from summed radiance × pixel area with the steradian term treated as 1 sr. Values from other software are not guaranteed to match. Validate cross-software comparisons; retain the metric, units, and ROI method with exported results.

5. Work through a survival example

Open Animals → Edit survival data (or Plot → Survival → Edit survival data…). Every animal also has its own survival Edit link in the Animals list. Check Dead / censored for a death date, and mark deaths unrelated to tumor as Non-tumor death (censor). For a living animal checked after its last BLI scan, enter Last known alive. To use one alive-check date for all animals without a recorded death, choose the date and click Apply to all without death; this replaces their existing alive dates but does not change death dates. Set Day 0 here if the study start differs from the first scan, then select Save dates. This fictional example uses September 1, 2026:

For this variation, C1 has no September 15 acquisition or assigned panel. Control survival drops to 50% at day 9; Treatment remains at 100% through its last observation. C2 has no BLI scan after September 15, but its September 20 alive check extends follow-up to day 19. Without a death date or an alive check after the final scan, the animal is censored at its last scan. A dated non-tumor death is censored on its recorded date.

Check censor ticks, the optional number-at-risk table, median guides, and the visible groups. The app reports group medians and a log-rank comparison across visible groups; this four-animal illustration is for learning the controls, not drawing treatment conclusions. Survival has its own CSV, SVG, and 300 dpi PNG exports.

6. Back up and share

Signed-out work saves in this browser on this device. Open an experiment and choose Download backup in the editor for a .sbli archive; use Import backup to restore one. Keep the original acquisition files too.

Sign in for private cloud backup and wait for Backed up. Free accounts keep 2 active cloud experiments, Plus keeps 10, and Unlimited has no experiment-count limit. Each cloud archive is limited to 1 GB. Failed backups offer Retry; local saving and confirmed cloud backup are separate states. Avoid editing the same experiment on multiple devices simultaneously.

Share creates a public view-only link to the latest cloud-backed experiment. Anyone with that link can browse and export its scans, results, groups, and imported metadata. Use Revoke link to disable access or Replace link to invalidate the old URL. Cloud deletion normally moves an experiment to Trash for 30 days; Delete forever is permanent.

Quick troubleshooting

• No signal plot: check quantitative import status, animal assignments, time points, and populated crop panels.
• A dim animal looks bright in Scans: check Normalized radiance; per-scan stretching is for inspection.
• Unexpected survival times: check acquisition dates, Day 0, death dates, and last-scan censoring.
• Missing figure cells: verify that you reused the same animal identity and selected the correct time point.
• Backup not confirmed: retain the local work, check the status and size message, and retry when connected.

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