Free browser-based BLI workflow · Updated September 12, 2026

IVIS bioluminescence analysis and longitudinal figure building

SimpleBLI turns supported IVIS acquisition folders into consistently scaled panels, ROI measurements, time-course plots, CSV data, and publication-ready figures. Nothing is installed.

Analyze IVIS data free Check supported files

The real app, on an anonymized real experiment

Let SimpleBLI do the repetitive work

Import a longitudinal study, let the beta detector propose mouse outlines, review them, then use the same experiment to build shared-scale figures and signal plots. The screenshots below show the actual browser interface running an anonymized real experiment.

SimpleBLI crop window showing the Auto-detect mice button and proposed dashed mouse outlines on an anonymized real IVIS photograph
Auto-trace large experiments. One click proposes individual mouse outlines from the photograph. Accept the good outlines, dismiss false detections, reshape where needed, and assign each mouse. Automatic detection and outline editing are beta features, so every proposal should be reviewed.
SimpleBLI Figure view arranging individual mice across three time points with one shared radiance color scale
Normalize every panel together. A shared radiance range and color bar keep animals and time points visually comparable.
SimpleBLI Plot view showing longitudinal total flux lines for control and experimental mice
Analyze without leaving the app. Plot total flux, mean radiance, or maximum radiance over time, then export the plot or underlying CSV.

What SimpleBLI is built to do

SimpleBLI covers the repetitive part of a BLI study: arranging animals across time points, keeping the display scale consistent, calculating comparable ROI summaries, and exporting one figure.

Normalize longitudinal IVIS images

Apply one shared radiance minimum, maximum, log or linear scale, colormap, and color bar across quantitative panels.

Measure BLI regions of interest

Keep measurement ROIs separate from display annotations and export total-flux estimates, mean radiance, maximum radiance, and CSV data.

Plot signal over time

Compare animals, controls, and treatment groups using dated time points, group-colored traces, and mean or median summaries.

Build publication-ready BLI figures

Arrange individual animals or whole scans, add labels and a shared color bar, and export the displayed figure as a 300 dpi PNG.

How to analyze longitudinal IVIS bioluminescence data

This workflow keeps quantitative measurements and figure assembly connected, and states explicitly which data is calibrated and which is rendered-only.

  1. Import acquisition foldersDrag in a study folder or select acquisition folders containing ClickInfo.txt and raw luminescent.TIF.
  2. Confirm quantitative statusSimpleBLI labels acquisitions as quantitative only when it can recover a usable calibration coefficient and exposure metadata.
  3. Define animals and groupsCrop animals, name subjects, assign control or treatment groups, and organize scans into dated time points.
  4. Normalize all panelsUse one robust-percentile or manually specified radiance range so color differences mean the same thing throughout the figure.
  5. Measure and plot ROIsChoose total-flux estimate, mean radiance, or maximum radiance and inspect individual or grouped time-course traces.
  6. Export figures and dataDownload the figure or plot as a 300 dpi PNG and export ROI measurements for downstream statistics.

IVIS file compatibility

Use the original acquisition folder whenever quantitative comparison matters. A screenshot or pseudocolor export may look correct but does not necessarily contain the calibration needed to recover radiance.

InputHow SimpleBLI uses itQuantitative?
ClickInfo.txt + luminescent.TIFReads acquisition metadata, raw CCD counts, exposure, binning, read bias, field of view, f-number, and the matching calibration coefficient.Yes, when the required metadata and coefficient are available.
photograph.TIFUses the white-light photograph as the anatomical background under the luminescent signal.Supports the overlay; radiance comes from the luminescent data.
Standalone TIFF, PNG, or JPEGImports the file as a rendered panel for layout and labeling.No. Rendered-only images cannot be rescaled quantitatively.
.amix or .auraxProject files with these extensions are not opened.No. Import the acquisition folder instead.
Compatibility note: IVIS acquisition folders vary across instrument generations and acquisition software versions. Confirm a representative acquisition in SimpleBLI before moving an entire study, and retain your original data and prior results.

What SimpleBLI does and does not do

Does

  • Imports supported IVIS acquisition folders (containing ClickInfo.txt and raw luminescent.TIF) and preserves calibrated radiance.
  • Crops and identifies animals across time points. Automatic mouse outlines are beta, so every outline must be reviewed.
  • Applies one shared display radiance scale across quantitative panels.
  • Measures ROIs: pixel count, area, mean, minimum, and maximum radiance, and a documented total-flux estimate.
  • Plots signal over time and Kaplan–Meier survival.
  • Exports figures and plots as PNG or SVG and measurements as CSV.
  • Runs in a browser, with no install and no account for local work.

Does not

  • Acquire images or control an instrument.
  • Calibrate fluorescence.
  • Perform 3D reconstruction, DLIT, FLIT, CT registration, or spectral unmixing.
  • Open .amix or .aurax project files.
  • Recover quantitative radiance from standalone TIFF, PNG, or JPEG, which are rendered-only panels.

Total flux vs average radiance in IVIS analysis

These measurements answer different questions. Record the metric, units, ROI method, and any background or normalization procedure in your analysis notes and figure legend.

Radiance

photons/s/cm²/sr

Calibrated signal per unit area and solid angle. Radiance is used to map BLI intensity and set a common display scale across quantitative panels.

Average radiance

photons/s/cm²/sr

The mean radiance of pixels inside an ROI. It describes typical surface brightness but can change when the ROI boundary changes.

Total flux

photons/s

Signal integrated over the ROI, computed from radiance, ROI area, and a solid-angle term. Used for whole-signal comparisons.

SimpleBLI total-flux caveat: SimpleBLI reports a documented estimate calculated from radiance and pixel area with the steradian term treated as 1 sr. Relative comparisons made with identical acquisition settings are the intended use. Absolute values from other software use different solid-angle conventions and are not guaranteed to match, so validate the metric before using it as a direct substitute.

IVIS bioluminescence analysis FAQ

Concise answers about free BLI software, supported files, ROI measurements, display normalization, privacy, and publication figures.

Is SimpleBLI free?

Yes. The analysis and export tools are free, and there is no installer or license key required. Paid plans increase active cloud experiment counts: Free keeps 2, Plus keeps 10, and Unlimited has no count limit. Each cloud backup is limited to 1 GB.

Can I analyze IVIS data without installing desktop imaging software?

For supported 2D acquisition folders, yes. SimpleBLI reads ClickInfo.txt and luminescent.TIF directly. Keep the acquisition software for instrument control, project editing, 3D, CT, spectral unmixing, and other specialized workflows.

What files are required for quantitative IVIS analysis?

A supported acquisition needs ClickInfo.txt plus luminescent.TIF. photograph.TIF is optional but provides the white-light background. Quantitative status also depends on usable calibration metadata.

Does SimpleBLI open .amix or .aurax files?

No. Project files with those extensions are not opened; import the acquisition folder instead. A rendered image export can be imported for layout only.

Is SimpleBLI a replacement for desktop imaging software?

No. It covers a focused subset of work: supported 2D data import, shared display radiance scales, ROI summaries, plots, and figure assembly. It does not acquire images or perform advanced analysis.

Can SimpleBLI normalize every IVIS image to the same scale?

Yes. Quantitative panels can share one minimum, maximum, logarithmic or linear mapping, colormap, and color bar. That prevents each image from using a visually misleading independent range.

Can I perform IVIS ROI analysis?

Yes. Measurement ROIs report pixel count, area, mean, minimum, and maximum radiance, a documented total-flux estimate, and signal above an optional threshold. Measurements export as CSV.

Can I use ImageJ for IVIS images?

ImageJ is useful for general image processing, but a rendered PNG or screenshot does not automatically preserve IVIS radiance calibration. Use original calibrated source data for quantitative work and validate any cross-software workflow.

Does SimpleBLI upload my scans?

Signed-out experiments stay in browser storage on the current device. Signing in adds private account-backed cloud backup. Review your institution’s data-handling requirements before using any web application.

Can I make publication-ready IVIS figures?

Yes. SimpleBLI exports the displayed figure and plot as 300 dpi PNG files, with shared scales, color bars, labels, treatment colors, and individual-animal or whole-scan layouts.

Does it support fluorescence, 3D DLIT/FLIT, or CT?

No. SimpleBLI is limited to 2D bioluminescence workflows. Use the acquisition software for image acquisition, fluorescence calibration, tomography, spectral unmixing, multimodal registration, or CT analysis.

Which metric should I plot over time?

Use a metric that matches the biological question and keep the ROI method consistent. Total flux estimates whole-ROI signal; average radiance describes mean surface brightness; maximum radiance emphasizes the brightest pixel region.

Build your first longitudinal BLI figure

Follow the tutorial with a worked two-group example, including crop autosave, group summaries, survival curves, and sharing.

Open SimpleBLI, create a free experiment, and drag in a supported IVIS acquisition folder. Your original files are not modified.

Open SimpleBLI free