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Comparison

Ilastik vs CellProfiler

Ilastik and CellProfiler both land on Depends.

Ilastik versus CellProfiler
CompareIlastikCellProfiler
VerdictDependsDepends
Best forLife scientists analyzing microscopy imagesHigh-content screening labs
Who it's not forProduction ML teams needing scale, deployment, or vendor supportQuick measurement of a handful of images
PrivacyNo known public vulnerabilities found in the sources reviewed.12No known public vulnerabilities found in the sources reviewed.
Support qualityCommunity forum support; no vendor SLACommunity forum only; NIH grant funded
Public sentimentLab researchers on Reddit and the forum use it for cell counting and segmentation, valuing the no-code approach while flagging hardware demands.10Users praise its power for batch image quantification but consistently complain about a punishing learning curve and installation friction.
Biggest gotchaExpect to budget for a good workstation; users report slowdowns on big images⁶Free means no SLA . support is the community forum, roadmap depends on grants

Pick Ilastik when

  • Life scientists analyzing microscopy images
  • Cell counting and segmentation without coding
  • Zero-budget academic labs
  • Pipelines feeding Fiji, napari, or CellProfiler

When Ilastik is not a fit

  • Production ML teams needing scale, deployment, or vendor support
  • General-purpose photo editing or design work
  • Buyers wanting SLAs or paid support . none exists
  • Cloud-first workflows . it's a local desktop app

Pick CellProfiler when

  • High-content screening labs
  • Cell Painting / morphological profiling
  • Batch analysis of thousands of images
  • Core facilities with zero software budget

When CellProfiler is not a fit

  • Quick measurement of a handful of images
  • Interactive whole-slide browsing . use QuPath
  • Teams needing vendor support or SLAs
  • No-code users; pipelines demand tuning

Sources

  1. ilastik . Aboutilastik.org
    official
  2. ilastik: interactive machine learning for (bio)image analysis . Nature Methodsnature.com
    review
  3. ilastik . Downloadilastik.org
    official
  4. ilastik GitHub repositorygithub.com
    official
  5. Image Segmentation Made Easy: A Guide to Ilastik for Non-expertstowardsai.com
    review
  6. Computer recommendation for better ilastik performance? . image.scforum.image.sc
    review
  7. Ilastik output .h5 to be read by CellProfiler has issues . image.scforum.image.sc
    review
  8. Pixel classification in ilastik . image.scforum.image.sc
    review
  9. Exporting annotations . discussion about format . image.scforum.image.sc
    review
  10. Ways to automate cell counting? . Reddit r/labratsreddit.com
    review
  11. ilastik Security . LFX Insightsinsights.linuxfoundation.org
    security
  12. Product security page . ilastikilastik.org
    security
  13. Ilastik Integration . KNIMEknime.com
    official
  14. Ilastik . napari plugin Alfa Cohortchanzuckerberg.github.io
    official
  15. Customizing a Model for Fiber Segmentation . Carpenter-Singh Lab, Broad Institutecarpenter-singh-lab.broadinstitute.org
    news
  16. CellProfiler official sitecellprofiler.org
    official