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STEP UP YOUR MORPHOLOGICAL CELL PROFILING GAME WITH AI
Background and Motivation
A fast approach for fully-automated Cell Painting image analysis and feature extraction from raw image data
Philipp Kainz1
, Bendeguz H. Zovathi1
, Phillip Clarke1
, Maria Roa Oyaga2
, Victor Wong2
, David Egan2
, Thomas Ebner1
1
KML Vision GmbH, 8020 Graz, Austria
www.kmlvision.com
2
Core Life Analytics BV, 5211 DA 's-Hertogenbosch, The Netherlands
www.corelifeanalytics.com
Reproducible morphological profiling, particularly for drug discovery, has become an essential tool for compound evaluation [1]. We describe a
novel approach for cell profiling using a fully-automated computer vision approach with IKOSA AI. Our main motivation is to make Cell Painting
[2] easily accessible for biologists without computer science knowledge. The primary objective of this work is to create a parameter-free, robust,
deep learning-based computer vision algorithm to achieve precise object segmentations for fully-automated high-content imaging.
Materials and Methods
Results
Conclusions and Outlook
Validation dataset Cells (n=62,560) Nuclei (n=58,290)
Precision 0.97 0.98
Recall 0.89 0.94
Average Precision 0.86 0.92
IoU 0.86 0.91
[1] S. N. Chandrasekaran et al., bioRxiv 2022.01.05.475090, 2023.
[2] M.-A. Bray et al., Nature Protocols, 11(9):1757–1774, 2016.
[3] Cell Painting Gallery, Available: https://registry.opendata.aws/cellpainting-gallery/, Accessed: May 2023.
[4] KML Vision GmbH, IKOSA (software), Graz, Austria, software available at https://app.ikosa.ai, Accessed: May 2023.
[5] AE. Carpenter et al., Genome Biology, 7:1-11, 2006.
[6] Core Life Analytics, Available: https://corelifeanalytics.com, Accessed: May 2023.
ground truth image (nucleus)
Our approach (nucleus)
ground truth image (cell)
Our approach (cell)
BR00117054-C21-5
Cell segmentation
BR00116991-N15-5
Highlights Nucleus segmentation
DMSO
(negative
control)
Homoharringtonine
Web-based
software platform
High availability. Access
anywhere, anytime.
Fully-automated
feature extraction
No programming
knowledge required
StratoMineR
integration
Optimized feature
selection
Robust computer
vision pipeline
Easily transfer to
other datasets
We expect a significant impact on
resource efficiency in drug discovery
and personalized medicine.
Cell Painting will be available soon
on the IKOSA platform for
high-throughput scenarios.
True-Positive (overlap≥50%) False-Positive (overlap<50%) False-Negative (overlap<50%)
True-Positive (overlap≥50%) False-Positive (overlap<50%) False-Negative (overlap<50%)
True-Positive (overlap≥50%) False-Positive (overlap<50%) False-Negative (overlap<50%)
True-Positive (overlap≥50%) False-Positive (overlap<50%) False-Negative (overlap<50%)
References
Sign-up for your IKOSA AI free trial today! View the poster online
higher is better
higher is better
higher is better
Intersection over Union, higher is better
Ground truth label generation from
Cell Painting Gallery JUMP-CP pilot
dataset [3] using U2OS and A549 cell
lines; 5 fluorescent (Mito, AGP, RNA,
ER, DNA) and 3 brightfield channels
Training a deep learning instance
segmentation model using the IKOSA
AI software [4] on a well-defined,
diverse subset
Morphological feature extraction
based on CellProfiler [5] cell painting
parameter groups
Feature prioritization using
StratoMineR software [6] by Core
Life Analytics (SLAS EU 2023 poster
number: 1084-A)
Validation & quality control:
Compare IKOSA AI with the
CellProfiler output

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Poster - STEP UP YOUR MORPHOLOGICAL CELL PROFILING GAME WITH AI

  • 1. STEP UP YOUR MORPHOLOGICAL CELL PROFILING GAME WITH AI Background and Motivation A fast approach for fully-automated Cell Painting image analysis and feature extraction from raw image data Philipp Kainz1 , Bendeguz H. Zovathi1 , Phillip Clarke1 , Maria Roa Oyaga2 , Victor Wong2 , David Egan2 , Thomas Ebner1 1 KML Vision GmbH, 8020 Graz, Austria www.kmlvision.com 2 Core Life Analytics BV, 5211 DA 's-Hertogenbosch, The Netherlands www.corelifeanalytics.com Reproducible morphological profiling, particularly for drug discovery, has become an essential tool for compound evaluation [1]. We describe a novel approach for cell profiling using a fully-automated computer vision approach with IKOSA AI. Our main motivation is to make Cell Painting [2] easily accessible for biologists without computer science knowledge. The primary objective of this work is to create a parameter-free, robust, deep learning-based computer vision algorithm to achieve precise object segmentations for fully-automated high-content imaging. Materials and Methods Results Conclusions and Outlook Validation dataset Cells (n=62,560) Nuclei (n=58,290) Precision 0.97 0.98 Recall 0.89 0.94 Average Precision 0.86 0.92 IoU 0.86 0.91 [1] S. N. Chandrasekaran et al., bioRxiv 2022.01.05.475090, 2023. [2] M.-A. Bray et al., Nature Protocols, 11(9):1757–1774, 2016. [3] Cell Painting Gallery, Available: https://registry.opendata.aws/cellpainting-gallery/, Accessed: May 2023. [4] KML Vision GmbH, IKOSA (software), Graz, Austria, software available at https://app.ikosa.ai, Accessed: May 2023. [5] AE. Carpenter et al., Genome Biology, 7:1-11, 2006. [6] Core Life Analytics, Available: https://corelifeanalytics.com, Accessed: May 2023. ground truth image (nucleus) Our approach (nucleus) ground truth image (cell) Our approach (cell) BR00117054-C21-5 Cell segmentation BR00116991-N15-5 Highlights Nucleus segmentation DMSO (negative control) Homoharringtonine Web-based software platform High availability. Access anywhere, anytime. Fully-automated feature extraction No programming knowledge required StratoMineR integration Optimized feature selection Robust computer vision pipeline Easily transfer to other datasets We expect a significant impact on resource efficiency in drug discovery and personalized medicine. Cell Painting will be available soon on the IKOSA platform for high-throughput scenarios. True-Positive (overlap≥50%) False-Positive (overlap<50%) False-Negative (overlap<50%) True-Positive (overlap≥50%) False-Positive (overlap<50%) False-Negative (overlap<50%) True-Positive (overlap≥50%) False-Positive (overlap<50%) False-Negative (overlap<50%) True-Positive (overlap≥50%) False-Positive (overlap<50%) False-Negative (overlap<50%) References Sign-up for your IKOSA AI free trial today! View the poster online higher is better higher is better higher is better Intersection over Union, higher is better Ground truth label generation from Cell Painting Gallery JUMP-CP pilot dataset [3] using U2OS and A549 cell lines; 5 fluorescent (Mito, AGP, RNA, ER, DNA) and 3 brightfield channels Training a deep learning instance segmentation model using the IKOSA AI software [4] on a well-defined, diverse subset Morphological feature extraction based on CellProfiler [5] cell painting parameter groups Feature prioritization using StratoMineR software [6] by Core Life Analytics (SLAS EU 2023 poster number: 1084-A) Validation & quality control: Compare IKOSA AI with the CellProfiler output