How to Successfully Conduct Morphological Cell Profiling With The Cell Painting Assay

The Cell Painting Assay: A Powerful Tool for Drug Discovery 

The Cell Painting Method is a high-content imaging technique used in cell biology and drug discovery. It involves systematic staining of cellular components using a combination of fluorescent dyes to visualize various subcellular structures and organelles.

The Cell Painting Assay involves growing cells in multiwell plates while treating each well on the plate with a specific compound molecule or gene perturbation. Being an image-based high-throughput technique, the Cell Painting Assay entails grouping or clustering unknown features based on similarities in their morphological profile. The profile of a particular well on the plate is estimated by calculating the median of a single-cell measurement for that well. (Rezvani et al., 2022)

A typical Cell Painting Assay protocol involves the following essential steps (Caceido et al., 2022; Cross-Zamirski et al., 2022):

• Cell culture seeding
• Compound treatment/ Perturbation
• Staining
• Imaging
• Pre-processing 
• Image analysis
• Normalization
• Morphological Profiling

Experiments using the Cell Painting method typically involve identifying cells and their components with a set of fluorescent dyes that selectively bind to different cellular structures, such as the nucleus, cytoplasm, and specific organelles. These dyes emit distinct fluorescent signals, enabling the visualization of multiple cellular components simultaneously. The stained cells are then imaged using fluorescence microscopy. This technology enables capturing detailed images of the cellular structures. (Bray et al., 2016; Bray et al., 2017)

Typically a maximum of six fluorescent stains is used across five imaging channels in order to identify eight cellular components: nucleus (DNA), endoplasmic reticulum (ER), nucleoli, cytoplasmic RNA (RNA), actin, Golgi, plasma membrane (AGP) and mitochondria (Mito). (Cross-Zamirski et al., 2022)

Once the images are acquired, advanced image analysis models and computational solutions are employed to analyze the Cell Painting data. The analysis includes image segmentation, whereby individual cells are identified and their boundaries delineated. Subsequently, various morphological features, such as shape, size, texture, and intensity, are extracted from the segmented cells. The sum of these characteristics forms what is known as a cellular profile. This type of profile encompasses quantitative measurements that are useful for phenotypic screening and evaluating the impacts of perturbations, such as drug treatments or genetic modifications. (Bray et al., 2016; Bray et al., 2017)

Cell Painting offers a generalized approach for morphological cell profiling, meaning it does not rely on any specific molecular markers or targets. Instead, it captures a comprehensive snapshot of cellular components through the combination of different fluorescent dyes. This enables researchers to explore multiple aspects of cellular biology simultaneously, providing a holistic view of cellular function and response. (Bray et al., 2016; Bray et al., 2017) Particularly in the field of drug screening the Cell Painting method enables predicting the toxicity of compounds based on image-level and profile-level measurements. (Cross-Zamirski et al., 2022)

The Cell Painting technique has gained popularity due to its ability to generate rich quantitative data on cellular morphology and subcellular organization. It has been applied in broad areas of research, including drug discovery, toxicology studies, phenotypic profiling, gene expression studies, and understanding disease mechanisms. By profiling cells based on the  Cell Painting Assay, researchers can access valuable information about the mechanisms of action (MoA), identify potential therapeutic targets, and make informed decisions in the development of new drugs and therapies. (Bray et al., 2016; Bray et al., 2017)

What is Morphological Cell Profiling?

Morphological cell profiling refers to the systematic analysis and characterization of cellular morphology, which includes metrics like the shape, size, texture, and spatial organization of cells and subcellular structures. This approach involves capturing detailed information about cellular features using imaging techniques, such as high-resolution microscopy, and extracting quantitative measurements to describe the morphological characteristics of single cells or cell populations. (Bray et al., 2016; Bray et al., 2017)

Morphological cell profiling plays a crucial role in understanding cellular behavior, elucidating the effects of perturbations (e.g., drug treatments, and genetic modifications), and identifying phenotypic changes associated with various biological processes, diseases, or experimental conditions. By quantifying a very large set of morphological features in an unbiased manner, researchers can gain insights into the underlying mechanisms driving cellular responses and identify potential therapeutic targets. (Bray et al., 2016; Bray et al., 2017)

The emergence of high-content imaging and automated analysis methods has made it possible to conduct extensive morphological cell profiling on a large scale. This allows analyzing numerous cells, ranging from thousands to millions, in a high-throughput fashion. By leveraging advanced image analysis solutions, based on machine learning, and computational methods, researchers can extract valuable information from complex image datasets. Such advances in technology enable the comprehensive characterization and comparison of cellular phenotypes. (Bray et al., 2016)

Morphological cell profiling is widely used in various fields, including drug discovery, toxicology, cancer research, developmental biology, and regenerative medicine.

It provides a holistic view of cellular structures and their alterations, aiding in identifying biomarkers, evaluating compound effects, classifying cell types, and understanding the complex interplay between cellular components. (Bray et al., 2016; Bray et al., 2017) It is important to distinguish morphological profiling from conventional screening assays. The differences between these methods lie in their scope and approach. While conventional assays focus on quantifying a limited set of predetermined markers that are known to be associated with specific biological features of interest, morphological profiling takes a broader approach allowing for a more generalizable method that can be applied across different scenarios. (Bray et al., 2016)

By adopting an unbiased approach, morphological profiling offers the opportunity for discovery without being limited by existing knowledge or preconceived notions. It enables researchers to explore a multitude of biological processes or diseases of interest within a single experiment. This broad applicability holds the potential for increased efficiency and resource utilization, as one dataset can yield valuable insights into multiple areas of research. (Bray et al., 2016; Bray et al., 2017)

While various high-content screening methods exist for generating comprehensive profiles of biological samples, such as metabolomic or proteomic profiling, Bray et al. (2016) argue that gene expression profiling is presently the sole practical alternative to image-based morphological profiling in terms of throughput and efficiency. However, gene expression profiling is limited to aggregating cell populations and cannot be performed at the single-cell level, unlike morphological profiling, which offers the advantage of obtaining profiles at the individual cell level. This possibility enhances the chances of detecting changes in subpopulations of cells. (Bray et al., 2016)

Fundamentally, morphological profiling offers a versatile and generic approach that crosses the boundaries of pre-existing knowledge. It empowers researchers to unveil novel co-dependencies, identify unforeseen correlations, and attain a more comprehensive understanding of cellular attributes. By embracing this unbiased methodology, researchers can fully harness the potential of their experimental data and explore uncharted paths of scientific inquiry.

Key Benefits of the Cell Painting Method

The Cell Painting Method offers several advantages as compared to traditional techniques in image analysis, making it a valuable tool for unbiased information gathering in various areas of research.

First and foremost, the Cell Painting Method stands out as an inexpensive technique compared to other approaches used for image analysis. By applying commonly used fluorescent dyes and stains, the Cell Painting Assay eliminates the need for costly reagents and specialized lab equipment, which makes it accessible to a broader range of researchers and institutions. (Bray et al., 2016; Bray et al., 2017)

Furthermore, it excels in providing rich information about cellular components and their spatial organization. Through the use of multiple fluorescent dyes, it captures comprehensive data on various subcellular structures, including nuclei, cytoplasm, and organelles. This holistic approach enables researchers to gain a more comprehensive understanding of cellular behavior and dynamics. In traditional analysis techniques, researchers often rely on specific targets to study cellular components or processes. This may require the use of specific antibodies or probes that bind to the desired targets, enabling their detection and visualization. However, this approach limits the analysis to a small number of predetermined analytes, as each marker is designed to detect a specific molecule or structure. (Bray et al., 2016)

In contrast, the Cell Painting Method relies on the inherent properties and characteristics of the cellular structures themselves, such as their morphology, texture, and spatial distribution. It provides a more holistic view of the cell, capturing a wide range of information beyond the low number of analytes targeted by traditional marker-based techniques. As a result, researchers can explore diverse cellular characteristics and uncover novel insights without being limited by predefined markers or targets. (Bray et al., 2016; Bray et al., 2017)

Another advantage of the Cell Painting Assay lies in its efficient utilization of a limited number of imaging channels. Leveraging a small set of fluorescent dyes significantly simplifies image acquisition and analysis. This streamlined approach reduces potential technical challenges, such as spectral overlap or photobleaching, while still providing valuable information for comprehensive cellular profiling.

The Impact of AI Technology on Cell Painting Image Analysis

Leveraging the power of artificial intelligence and automated image analysis enables researchers to extract valuable information from large-scale image data. Among these technologies, Cell Painting image analysis solutions have emerged as powerful tools for comprehensive cell profiling. By automating the extraction of single-cell morphological features from complex microscopy images, this approach facilitates an unbiased and effective way for the measurement of cellular dynamics. (Bray et al., 2016)

Automated Analysis with Image Segmentation

One key aspect of image-based cell profiling is image segmentation, the process of partitioning an image into meaningful regions. Cell Painting analysis solutions utilize advanced image segmentation algorithms to accurately identify individual cells within a heterogeneous population. This automated process ensures precise delineation of cellular boundaries and enables subsequent analysis at the single-cell level.

Comprehensive Morphological Profiling

The strength of the Cell Painting approach lies in its ability to perform automated feature extraction and quantify a wide range of morphological characteristics. By analyzing multiple parameters, including shape, size, intensity, texture, and measurements of adjacency between cellular structures, the software generates morphological profiling data that provides a detailed description of cellular properties.

Harnessing the Power of Automated Analysis and Image Segmentation

One key aspect of image-based cell profiling is image segmentation, the process of partitioning an image into meaningful regions. Cell Painting image analysis solutions utilize advanced segmentation models to accurately identify individual cells within a heterogeneous population. This automated process ensures the precise delineation of cellular boundaries and enables subsequent analysis at the single-cell level.

Enhancing The Capabilities Of Morphological Cell Profiling

The strength of AI-driven Cell Painting data analysis lies in its automated feature extraction capability and enabling the quantification of a wide range of morphological characteristics. By analyzing multiple parameters, including shape, size, intensity, texture, and measurements of adjacency between cellular structures, the software generates morphological profiling data that provides a detailed description of cellular properties.

Transfer learning for improved generalizability 

Integrating transfer learning techniques can enhance the generalizability of image-based cell profiling. By using pre-trained AI models and knowledge gained from one dataset, these approaches enable the efficient adaptation of the learned features to new image data and experimental conditions. This transfer learning capability allows researchers to leverage existing knowledge and models, reducing the need for extensive data collection and accelerating the analysis process and robustness of the trained model.

Automation Is Key to Efficiency and Scalability in Cell Painting Data Analysis

AI-driven software offers an efficient and scalable solution for analyzing large-scale microscopy datasets. Automating the extraction of morphological features from thousands or even millions of cells significantly reduces the time and effort required for data analysis. This enables researchers to uncover patterns and make discoveries at an unprecedented scale, accelerating scientific progress in fields such as drug discovery and personalized medicine.

Effective Strategies for the Evaluation of Cell Profiling Data

Evaluation plays a crucial role in the success of cell profiling techniques. To ensure the accuracy and reliability of the obtained results, effective strategies for data evaluation are essential. Here, we discuss some key approaches that can be employed for the evaluation of cell profiling data:

Ground Truth Comparison As An Indicator Of Validity

One of the fundamental strategies to test the validity of your results is comparing the cell profiling results with a ground truth dataset. This involves validating the identified cells and their morphological features against manually annotated and expert-verified data. By quantitatively measuring the coincidence between the automated analysis results and the ground truth, researchers can assess the accuracy and performance of the cell profiling models

Which Metrics Help You Assess the Quality Of Your Model

Incorporating quality control metrics is essential to ensuring the reliability of cell profiling data. These metrics assess various aspects of the image acquisition and analysis process, such as image quality, segmentation accuracy, and feature consistency. By monitoring and evaluating these metrics, researchers can identify and address potential sources of variability or bias, leading to more robust and reproducible results.

Benchmarking and Comparative Analysis

Benchmarking cell profiling methods against established standards or alternative approaches is a valuable strategy for evaluating their performance. By comparing the performance metrics, computational efficiency, and accuracy of different models or software solutions, researchers can make informed decisions about the most suitable approach for their specific research objectives. Comparative analysis enables the identification of strengths, weaknesses, and areas for improvement in cell profiling methodologies.

Validation with Independent Datasets

Validating cell profiling results using independent datasets provides an additional layer of confidence in the findings. By running the developed models or software applications on new datasets, researchers can assess the generalizability and robustness of their approaches across different experimental conditions, imaging platforms, or biological systems. These validation steps ensure that the cell profiling techniques perform consistently and reliably beyond the training dataset.

Statistical Analysis

Statistical methods are commonly employed to analyze and interpret cell profiling data. These techniques enable researchers to identify significant differences between experimental groups, evaluate the variability within samples, and determine the statistical significance of observed changes in morphological features. Caicedo et al. (2017) provide a very comprehensive overview of existing data-analysis strategies for image-based cell profiling. For example, correlations and hierarchical clustering are methods commonly used to group different perturbations together. Correlation analysis helps identify profile similarities according to feature type, cell component, and imaging channel. (Caceido et al., 2022, Cross-Zamirski et al., 2022)

The development of modern devices, equipped with multiprocessing capabilities, automation, and robotics, has enabled researchers to rapidly evaluate a substantial number of samples. This has significantly improved efficiency and productivity in screening experiments. Unlike earlier technologies that sacrificed resolution or content during accelerated processing, contemporary devices empower researchers to capture a vast amount of data with high quality. This revolution in high-content screening devices has created a pressing need to efficiently detect relevant images from massive datasets, addressing challenges in accelerating and automating the analysis processes.

Presenting Our Approach To Automated Morphological Cell Profiling

To tackle the existing challenges in cell profiling, we propose an efficient AI-driven workflow to analyze Cell Painting image data with the help of the IKOSA software. Our specialized app for morphological cell profiling is a product of our collaborative efforts with the Dutch company CoreLife Analytics, a leading provider of analytical Cell Painting solutions.

Congratulations to Bendegúz H. Zováthi, an international Master’s student of Image Processing and Computer Vision, at Pázámány Péter Catholic University (PPCU), University Autónoma de Madrid (UAM), and University of Bordeaux (UBx) on the successful completion of his Thesis titled “Morphological cell profiling by segmentation-based feature extraction.” During his internship at our company, KML Vision GmbH, Bendegúz significantly contributed to the development of our IKOSA Cell Painting App. His dedication and expertise have been invaluable, and we are thrilled to have been part of his academic journey.

Materials and Methods

We offer a comprehensive overview of the methods we have used to prepare the Cell Painting image data. By adhering to a well-established protocol we have been able to construct a robust and highly efficient image analysis solution based on image segmentation and feature extraction. The set of images employed in the development of the IKOSA Cell Painting App has been rigorously validated by experts and made available by the JUMP-Cell Painting Consortium. This publicly accessible dataset provides immense value for a diverse array of research areas.

Dataset

For the App development, we utilized a carefully selected subset of the CPG0000-jump-pilot dataset from the Cell Painting Gallery. This subset served as both training data and a benchmark for our project. This publicly available image database involves profiling A549 and U2OS cells at various time points. The A549 cell line originates from lung carcinoma epithelial cells obtained in 1972. The U2OS cell line, on the other hand, is an epithelial morphology cell line established in 1964. In 2022, Chandrasekaran et al. introduced the CPG0000-jump-pilot dataset, which serves as a valuable reference for evaluating methods, predicting compound similarities, and assessing perturbation effects. The authors emphasize in their article that this carefully compiled and well-annotated dataset is intended to accelerate the advancement of novel medicines and therapies.

The CPG0000-jump-pilot database consists of all the necessary files and information for image analysis including the CellProfiler pipeline utilized for processing. It comprises fluorescence microscopy images as presented in Figure 1 and corresponding analysis outputs from the Cell Painting Assay. These outputs include segmentation outlines (in PNG format), extracted features (in CSV format), and associated metadata (in both CSV and TXT formats). Besides the fluorescent channels, this database incorporates brightfield images that offer additional insights into cell morphology and texture.

The dataset consists of uncompressed 16-bit TIFF files, offering a resolution of 1,080×1,080 pixels. To label different cellular compartments or structures, five distinct fluorescent stains have been used, as outlined in Table 1.

Quality Control Metadata

The careful selection of training data plays a crucial role in the development of deep learning applications, as it directly impacts the performance and accuracy of the model. High-quality data is essential to ensure the reliability of the resulting model, whereas noisy, incomplete, or damaged data can compromise its effectiveness. The Cell Painting Gallery is a huge dataset library carefully generated in cooperation with leading pharma companies and experts.

In collaboration with our partner Core Life Analytics, we aimed to capture the maximum phenotypic diversity within the available data for our Cell Painting model development. Therefore, we carefully selected a diverse and representative subset consisting of 2780 images, totaling approximately 90 GB in size. This image subset was chosen to ensure comprehensive coverage of different cellular phenotypes for optimal model training.

App Development and Image Analysis 

The development phase of the app can be conceptualized as a two-step process, involving image segmentation and feature extraction. During segmentation, the app identifies and delineates individual cells and their nuclei. The subsequent feature extraction measures morphological features for each cellular compartment.

The IKOSA deep neural network has been trained to perform accurate nuclei and cell segmentation using the segmentation outlines generated by CellProfiler as ground-truth annotations (Figure 2).

CellProfiler uses image processing models, whereby the segmentation is executed on low-level features (for example thresholding based on intensity level). One notable contrast is that our approach utilizes deep learning, where the model has been specifically created to autonomously recognize relevant features based on training input data. This deep learning-based segmentation builds upon more complex and generic profile features, resulting in a more robust and reliable model. Deep learning enables the model to adapt to variations present in the data and to capture intricate patterns. This approach offers greater flexibility and adaptability, ultimately enhancing the accuracy and performance of our image segmentation solution.

To validate the results obtained with the trained model a comparison with the widely acknowledged CellProfiler pipeline has been conducted, which is considered state-of-the-art. This validation aims to assess the performance and effectiveness of our model in accurately delineating cells and identifying different cellular features.

Results

To assess the performance of the trained model, a comprehensive evaluation of the segmentation output has been conducted. This evaluation utilizes both qualitative and quantitative measures to analyze the results. Furthermore, a thorough comparison of the extracted features with the state-of-the-art JUMP-CP pilot dataset has been conducted, providing a comprehensive analysis of the app’s performance.

Segmentation Evaluation

The instance segmentation model has been trained using 8 imaging channels (5 fluorescence, 3 brightfield). The training data comprises a total of 2,208 images with 215,732 nucleus labels and 231,501 cell labels. The validation data consists of 572 images with 58,290 nucleus annotations and 62,560 cell annotations.

The model demonstrates efficient performance by producing predictions for a 1,080×1,080 pixel-sized image in just 2.2 seconds. The quantitative evaluation, as presented in Figure 3, indicates that the model achieves a high level of accuracy in precisely identifying cell- and nuclei instances. It also exhibits only a low rate of False Positives, indicating its effectiveness in distinguishing instances.

As regards qualitative evaluation, Figure 4 showcases the precise nucleus segmentation outputs generated by our model, surpassing the ground truth data obtained from CellProfiler.

The reported False Positive detections on the right side of the image are actually True Positive predictions. In contrast, the ground truth annotations in this case were incorrect (cluster of four cells). The model’s cell segmentation results have been improved by utilizing nucleus segmentation to separate cell instances, as depicted in Figure 5.

However, it should be noted that while this approach is not able to achieve perfect detection of all objects (which is barely the case in bioimage analysis), it only results in a small number of False Negative detections and shows a really good overall outcome.

Further, it is important to emphasize that the ground-truth labels used in the training data are not perfect or entirely error-free.

Additionally, it is worth mentioning that we also trained a segmentation model using only 5 channels. The latter yields similar accuracy levels as compared to the model trained with 8 channels. Surprisingly, the inclusion of brightfield images in the 8-channel model did not have a significant impact on the overall performance of the model. This observation suggests that the additional information provided by the brightfield images may not be crucial for achieving high segmentation accuracy in our specific case.

Comparison of extracted features

To obtain an information-rich morphological profile of the cells, it is recommended to utilize as many channels as possible. This approach provides comprehensive measurement outputs on various object feature groups, including area and shape, correlation, granularity, intensity, location, neighbor, radial distribution, and texture.

In order to compare the features extracted with our model with those detected with CellProfiler, the normalized mean squared error (MSE) and mean absolute error (MAE) have been calculated for all objects.

The overall MSE results point to a value of 0.011, while the MAE value is 0.029. These results demonstrate the effectiveness of our approach.

How the IKOSA Cell Painting App outperforms CellProfiler

User-friendly: The IKOSA Cell Painting App enables users to examine cell profiling image data without the need for programming skills or specialized hardware. Also, its browser-based interface ensures accessibility and flexibility, allowing users to conveniently conduct Cell Painting analysis from any computer with an internet connection.

Fast and automated image analysis: Configuring complex image analysis pipelines can be a time-consuming process, often taking several days, even for experts in the field. With the IKOSA Cell Painting App, this lengthy configuration is eliminated. The App offers a novel approach to image analysis, enabling rapid feature extraction from raw image data, automating and streamlining the analysis process. This saves valuable time and resources.

Robustness and performance: The IKOSA Cell Painting App employs a computer vision approach that ensures robust data analysis and high performance, overcoming the challenges associated with conventional threshold-based methods.

Transferability and Reusability: The trained model can be transferred and retrained on other datasets. This flexibility enables our solution to be applied to a broad range of experiments, enhancing the scope of the Cell Painting Assay.

Collaboration with Core Life Analytics: The App’s functionality is further improved through its compatibility with the StratoMineR software. This collaboration enables optimized feature selection without losing any relevant information, providing researchers with a streamlined and efficient analysis workflow.

Resource efficiency: The App’s high throughput, combined with automated analysis capabilities contribute to more efficient screening processes and data-driven decision-making. And all this without investing in additional IT infrastructure.

Dedicated support and maintenance: While open-source software relies on community support for maintenance and updates, the IKOSA Cell Painting App offers dedicated support and ongoing maintenance from our development team. This ensures prompt bug fixes, updates, and improvements, providing users with a more reliable and supported platform for their image analysis needs.

Discussion

During the development process of the IKOSA Cell Painting App, our team gained a comprehensive understanding of the requirements and challenges associated with the Cell Painting method. In-depth research has been conducted to identify shortcomings in existing tools and explore novel approaches. Subsequently, the conceptualization and design phase has taken place, outlining the core features and workflow of the App.

Developing accurate and efficient software solutions by employing advanced computer vision techniques and deep learning models is crucial to the success of a Cell Painting experiment. In our case, extensive testing and optimization have been performed to enhance software performance and minimize processing requirements.

Thorough quality assurance procedures have been implemented to guarantee the stability, accuracy, and reliability of the App. Continuous maintenance, updates, and feedback collection are in progress to facilitate ongoing improvements that address evolving research requirements.

It is necessary to mention that the “ground truth” data used for developing our model is derived from the Cell Painting Gallery data, including the object outlines and pixel coordinates. During the data preprocessing stage, the segmentation outlines have been converted into masks, which may introduce slight variations or differences compared to the original outlines. That being said, the “ground truth” in this context does not imply an absolute representation of the actual ground truth. Instead, it refers to data generated by another image analysis software (CellProfiler). Although the data has undergone meticulous validation by experts, it is essential to acknowledge that absolute correctness cannot always be guaranteed due to the complexities and nuances inherent to image analysis.

The IKOSA Cell Painting Application is the most robust and universal solution on the market. With this versatile approach to morphological profiling, we aim to provide users with a tool that has a substantial positive influence on drug discovery and personalized medicine.

Get ahead with IKOSA!

For more information about the IKOSA Cell Painting App, feel free to reach out to us. Our team is here to answer your questions, provide assistance, and guide you through the exciting world of advanced cell profiling. Join us on this journey of discovery and unlock the full potential of your research data. Contact us today and experience the future of morphological cell analysis with IKOSA!

Our authors:

Benjamin Obexer

Lead content writer, life science professional, and simply a passionate person about technology in healthcare

Elisa Opriessnig

Content writer focused on the technological advancements in healthcare such as digital health literacy and telemedicine.

Fanny Dobrenova

Health communications and marketing expert dedicated to delivering the latest topics in life science technology to healthcare professionals.