Analysis

Quick analysis

Upload your microscopy images, choose the analysis and get the results. Use Experiments for conditions, controls and measurements over time.

Upload images and review

Analyzing the same field over time? Track a time-lapse instead.

Start from your lab's saved setup. You can still change any field for this run. Manage protocols

What are you measuring?

Choose the known assay for the clearest report. Not sure? Ask Auto for a suggestion, then confirm the analysis type.

Beta workflows are available for early use. Review their results before scientific decisions.

Review the suggested analysis

Review every image. If they need different assays, run them separately.

Confirm fluorescence channels

Choose one nuclei channel and name each marker. Marker intensity is measured inside each nucleus. Suggestions come from channel names; confirm every role before analysis.

Reading channel metadata…

A pipeline file fills in the channel roles and measurement settings from an earlier analysis. You still confirm the channels and choose this run's control images.

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Settings this file applies

This file was changed after it was exported.

The analysis tools have been updated since this file was exported. Results may differ from the original run.

Preview from the first image; these channel indices apply to every selected file. Confirm that control and test images use the same acquisition settings.

Negative-control images

Declare the images without marker signal. Positivity uses the 99th percentile of their background-subtracted nuclear means. Without usable controls, results need review and no percentage is available.

Channel plan confirmed. Analysis uses the nuclei channel and the named nuclear markers.

Tip: upload images without burned-in scale bars when possible. We auto-suppress opaque bars before counting, but cells in that region are excluded from the count. Acquiring without the bar gives the most accurate total. Upload guide.

images ready

Analysis has not started. These checks cannot establish measurement accuracy.

Analysis Settings

Analysis model

Trained for:

Recommended/default models are shown first, followed by custom models trained for your account.

Your chamber volume and dilution combined. We multiply the cell count by this and show cells/mL alongside it.

Leave pixel size at 0 to use the scale in stage-coordinate filenames. A supplied pixel size overrides the filename scale.

Not yet validated. Stage coordinates place the tiles; objects outside a detected well edge are excluded. Check each overlay. For an image without coordinates, add its pixel size.

Microscope calibration

Cell counts still work without this. Density (cells/mm²) needs a real µm/pixel; cells/mL comes from the cells-per-mL multiplier you enter for suspension counts.

Cell counts still work without this. Density (cells/mm²) needs a real µm/pixel; cells/mL comes from the cells-per-mL multiplier you enter for suspension counts.

Areas will be computed from this calibration instead of an assumed field size.

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Calibration is unavailable for these images; count/confluency can still run.

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Batch tools

Export, bundle, and retry

Selected job ID (for bundle/retry):

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Latest jobs (progress)

Pick Job Status Progress Created