Genedata Imagence®

for HCS Image Analysis

Developed in partnership with leading pharmaceutical companies, Genedata Imagence is an advanced deep learning-based software solution for the automation of image analysis that is revolutionizing High Content Screening (HCS). Now, every biologist can easily take control and analyze HCS outcomes, enabling the broad application and scale-up of HCS. This award-winning solution uses deep learning to automate feature extraction and phenotype classification, drastically reducing image analysis time while delivering high-quality, reproducible results.

Classical vs. Deep Learning-based Workflow

(FIG. 1) A) The classical HCS workflow includes many steps, several professional competencies, and continuous itera-tions, resulting in an HCS campaign that can take up to sev-eral months. B) Genedata Imagence for HCS image analysis shortens the time required from experiment to results while simplifying the entire process. Workflows can be reduced to just weeks as deep learning enables more experimental conditions allowing for a more rapid assay development. Moreover, Genedata Imagence allows scientists to fully automate the workflow and benefit from high-throughput screening campaigns. As soon as images are acquired, the trained CNN network is automatically applied, data is analyzed, and results are reported.

BiologistSetting up

image analysis

Establishing

imaging assaySelecting hits

Weeks

Report ResultsTrain and apply

CNN

Deep Learning-based HCS Workflow

Months

Report ResultsAnalyze Data Interpret DataAnalyze Images

Classical HCS Workflow

BiologistSelecting hits

BiologistReviewing

phenotypes

BiologistEstablishing

imaging assay

BioinformaticianSetting up

image analysis

BioinformaticianReducing features

Clustering phenotypes

A

B

Scalability

Genedata Imagence supports on-demand cloud computing service providers such as Amazon Web Services (AWS), and hy-brid deployments, allowing organizations to cost-efficiently scale-out the compute, even from multiple geographic locations and users. This infrastructure model never reaches its limits as it expands easily and contracts when the workload decreases. The system is constantly adapting to the needs of the whole orga-nization while ensuring high performance and parallelization for fast computations.

Fully Automated Workflow

Streamlining and automating the work-flow are key challenges in HCS image analysis. The many steps and profes-sional competencies required render a cumbersome process (Fig. 1A). With Genedata Imagence and its integra-tion with Genedata Screener®, it is now possible to fully automate HCS image analysis. The result: project cycle times are significantly shortened and a single biologist is empowered to run the work-flow from end-to-end, bypassing compli-cated analysis set-ups and many manual steps (Fig. 1B).

New Insights

Classifying phenotypes is an arduous task that requires expertise and intimate knowledge of cells and experimental conditions, and often only expected phenotypes can be found and classified. With Genedata Imagence, phenotypes are grouped based only on similari-ties in the experimental images (Fig. 2), and scientists can base their phenotype identification on the network's unbiased grouping combined with their biological expertise. This way, the potential to find previously unnoticed phenotypes and gain new insights significantly increases.

Genedata Imagence for HCS Image Analysis

(FIG. 2) Cell Painting Assay. A) The Object Similarity Map, which groups cells according to phenotypic similarity, can be color-coded based on metadata such as controls, compounds, and concentrations. The cell images corresponding to each point in the map can be selected and viewed next to the metadata, which allows investigation of the different cell populations in the dataset, and provides a visual impression of cell abundance depending on the compound treatment. B) Using gating tools, groups of similar cells can be selected from the map for training data on the phenotype of interest. The training datasets for all phenotypes can then be reviewed side by side in a dedicated user interface.

B

A

Interactive Data Exploration

Original images are accessible at all stages of the workflow for rapid QC and data exploration. Scientists can compare images, adjust the training sets in a few clicks, and apply the trained network to any new set of images without expertise in image analysis software.

Genedata Imagence seamless integra-tion with Genedata Screener allows the immediate assessment of the results validity due to measures such as IC50 or Robust Z', which facilitate data interpre-tation.

Reliability

Deep learning helps circumvent the oftentimes unavoidable lack of consis-tency that can affect data interpretation and decision making. Consistent applica-tion of the same trained network to new screening batches secures reproducible and reliable HCS image analysis. More-over, incremental learning allows you to readjust the network to address batch-to-batch variability, given, for example, due to differences among batches of primary cell lines. Genedata Imagence ensures confidence in the output of your research thanks to a more consistent analysis.

Solution of Choice

Genedata Imagence is the first com-mercially available solution for deep learning-based HCS image analysis. Its leadership in the field is recognized with Bio-IT World's Best of Show and Best Practices Awards.

Independent of the instruments used, Genedata Imagence allows harmoniza-tion and standardization of workflows across the entire organization. This vendor-agnostic software is cost-effec-tive, scalable, and shortens project cycle time, boosting research productivity.

Services and Support

Genedata offers a range of services and support, from installation and customization to global roll-out support, training, data analysis, application consult-ing and IT consulting services, all tailored to the specific needs of your organization. Our services team consists of highly skilled professionals with extensive domain knowledge in screening and soft-ware technology, bringing specialized know-how and experience to your organization.

Genedata

Genedata transforms life science data into intelli-gence with a portfolio of advanced software solu-tions and scientific consulting. With award-winning platforms, combined with deep domain expertise, Genedata enables dramatic increases in productivity and quality of research, development, and produc-tion. Founded in 1997, Genedata is headquartered in Switzerland and has offices in Germany, Japan, and the US.

Experienced Partner

With nearly two decades of experience in indus-trial screening data analysis and global enterprise deployments of Genedata solutions, Genedata is an ideal collaboration partner for companies wanting to advance their operations. In addition to the steadily evolving solution platforms, Genedata offers exten-sive opportunities for custom or co-development of specific new functionalities, procedures, or method-ologies to support your current and future needs.

Next Steps

To find out more about Genedata Imagence for HCS Image Analysis please visit www.genedata.com/imagence.

For a conversation about your image analysis needs or to schedule a live demonstration, please contact us at imagence@genedata.com.

Genedata Imagence® is part of the Genedata portfolio of advanced software solutions that serve the evolving needs of drug discovery, industrial biotechnology, and other life sciences.

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