Fluorescence microscopy image analysis for nuclei, markers, and colocalization.
Quantify markers, channels, nuclei, and colocalization while keeping overlays reviewable.
What this page covers
Use this page when the signal comes from fluorescence channels, confocal or widefield images, multiplex marker panels, or microscopy workflows that need logged thresholds and ROIs.
Talk through your images
Share the channels, marker names, example images, and whether the endpoint is count, intensity, colocalization, or positive-cell classification.
Request a meetingMeasurements
- Nuclear count
- Marker-positive count
- Intensity
- Pearson r
- Manders M1/M2
- Viability percent
Review outputs
- Channel overlays
- ROI logs
- Threshold records
- Per-cell tables
Image inputs, QC, and outputs
Use this section to decide whether the page matches your assay before requesting a meeting. The goal is to preserve the biological endpoint while making the image analysis repeatable, reviewable, and exportable.
Image inputs
Fluorescence microscopy analysis starts with representative images that match the endpoint your lab reports. Include controls and edge cases so thresholds can be set against real biological variation, not only ideal fields.
- Primary measurements: Nuclear count, Marker-positive count, Intensity, and Pearson r
- Matched positive and negative controls when available
- Consistent magnification, channel order, plate layout, or time-point labels
QC and validation
Each workflow should leave a visible trail from raw image to measurement. Review masks, thresholds, and flagged fields before exporting the final table.
- Raw image and overlay review before batch export
- Locked settings for repeated plates, stains, or time points
- QC flags for dim signal, merged objects, uneven background, or failed segmentation
Outputs for analysis
ConductVision should return both visual evidence and structured data so the result can be checked, summarized, and reused in downstream statistics.
- Typical outputs: Channel overlays, ROI logs, Threshold records, and Per-cell tables
- Per-image, per-cell, per-object, or per-well tables where relevant
- CSV exports for Prism, Excel, R, Python, or LIMS handoff
Workflows to start from
Open an existing ConductVision page when the workflow already exists, or request a meeting when your assay needs custom thresholds, outputs, or validation rules.
Nuclei fluorescence
DAPI or Hoechst nuclei segmentation with count, area, and intensity outputs.
Cell count fluorescence
Fluorescent object counts with batch overlays and per-image summaries.
Live/dead viability
Dual-channel live/dead segmentation for viability and dose-response readouts.
Fluorescence colocalization
Pearson, Manders, Costes thresholds, ROI batch analysis, and channel overlays.
Related Life Science pages
Use these pages to move between adjacent assays, specialist microscopy workflows, and the full Life Science atlas.
Request a Life Science meeting
Share your assay, representative images, and the measurement you need so the team can map the closest ConductVision workflow.
Microscopy center
Open specialist microscopy pages for stereology, atlas registration, vessel analysis, prep, and spines.
Life Science atlas
Return to the full biology application atlas for cells, assays, tissue, microscopy, and morphology.
Frequently asked questions
These answers cover the practical questions labs usually ask before sending example images or requesting a ConductVision workflow review.
What images work best for fluorescence microscopy analysis?
Use representative images from the same microscope, scanner, plate reader, or camera setup used in the study. The most useful examples include controls, typical fields, difficult fields, and any cases that affect Nuclear count, Marker-positive count, Intensity, and Pearson r.
Can ConductVision handle custom fluorescence microscopy endpoints?
Share the channels, marker names, example images, and whether the endpoint is count, intensity, colocalization, or positive-cell classification. ConductScience can confirm whether an existing workflow fits or define custom segmentation, thresholding, review, and export rules for the assay.
What results are usually exported from this workflow?
The expected deliverables include Channel overlays, ROI logs, and Threshold records, plus structured tables for downstream analysis. The page also lists the specific measurements and review outputs that are most relevant to this application.
Find out if ConductVision fits your fluorescence microscopy workflow
Send representative images, assay details, and the measurement endpoint. ConductScience can confirm the closest existing workflow or scope a custom analysis path.
