Cell painting image analysis for phenotypic profiling.
Extract marker and morphology features from multiplex cell painting images.
What this page covers
Use this page for high-content cell painting assays where nuclei, cytoplasm, organelle, and morphology features need to be measured consistently across plates.
Talk through your images
Bring the channel list, plate format, example images, and the phenotype classes or features you want compared.
Request a meetingMeasurements
- Nuclear features
- Cell shape
- Marker intensity
- Texture
- Positive fraction
- Plate-level summaries
Review outputs
- Multichannel overlays
- Per-cell feature tables
- Plate maps
- Phenotype exports
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
Application 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 features, Cell shape, Marker intensity, and Texture
- 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: Multichannel overlays, Per-cell feature tables, Plate maps, and Phenotype exports
- 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 and cell segmentation
Separate nuclei, cells, and marker-positive regions across channels.
Feature extraction
Measure intensity, area, shape, texture, and marker distribution.
Batch comparison
Export per-cell and per-well results for treatment-level analysis.
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.
High-content screening
Scale cell painting features across plates and treatments.
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 application 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 features, Cell shape, Marker intensity, and Texture.
Can ConductVision handle custom application endpoints?
Bring the channel list, plate format, example images, and the phenotype classes or features you want compared. 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 Multichannel overlays, Per-cell feature tables, and Plate maps, 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 application workflow
Send representative images, assay details, and the measurement endpoint. ConductScience can confirm the closest existing workflow or scope a custom analysis path.
