Accelerating drug discovery: The impact of ultra-fast screening

High content screening

This paid-for advertorial by Araceli Biosciences appeared in DDW Volume 25 – Issue 3, Summer 2024.

Accelerating discovery with real-time laboratory data 

In the era of artificial intelligence (AI), biotech R&D is hungry for data like never before. Machine learning (ML) is transforming innovation: faster discovery, better designs, reduced risk of clinical translation. But the ML model is only as good as the training data it learns from, and the AI strategy only as powerful as the data engine that drives it. Obtaining high volume, quality data to train these models is a must, and at Ginkgo Bioworks we are leading the way to fuel researchers’ pipelines with high quality biological data delivered in record time.

Scaling operations with ultra-fast high content imaging

To do this, we onboarded the Araceli Endeavor® high content imaging system (Figure 1) which is currently being integrated onto a newly constructed Reconfigurable Automated Cart (RAC) system. With this fully automated setup, our team will asynchronously schedule multiple imaging protocols, allowing assays to run 24/7. In so doing, we will deliver high-quality, high-speed image acquisition and analysis for functional genomic and phenotypic screens. Ginkgo’s requirements for cell-based imaging in large screening campaigns were speed and quality – both of which were easily satisfied with the Endeavor platform.

Figure 1. Modified Cell Painting protocol for 4-channel acquisition performed on the Endeavor (20x objective) and another HCI instrument (10x objective). Subregions of 200µm2 were sampled from the origin, unprocessed images (Endeavor, 700 pixels2; HCI, 290 pixels2). Images are presented as colour overlays on the DAPI channel.

Cell painting use case: maintaining image quality at nine times the speed

Cell painting, one of the most widely used assays for phenotypic screening in early drug discovery, is among the first use cases for our new imaging setup. A direct comparison (the same Cell Painting plate, Figure 1) of the Endeavor with an alternate high-content system revealed the Endeavor to be at least 9x faster. With both systems configured to acquire an entire 96-well plate with approximately 80% well coverage, using laser-based autofocus at each field of view and with four wavelengths captured, the Endeavor took only 10 minutes compared with the alternate HCI, which took 90 minutes. This dramatic increase in speed, with no loss of image quality or focus, permits a considerable increase in batch processing using a single instrument. Furthermore, because the Endeavor uses a high numerical aperture 20x objective greater image resolution (Figure 1) was obtained with a configuration optimized for speed of acqusition (Table 1).

Table 1. Acquisition configuration for two HCI systems for Cell Painting.

Advancing drug discovery screening without compromise

The implementation of this new high throughput system with the Endeavor will generate stellar results and revolutionise laboratory operations at Ginkgo Bioworks, allowing us to provide high-quality data to researchers faster than ever before. Our team is excited to unlock new assays and capabilities with this cutting-edge technology to deliver cell-based imaging as a service.

About the author

John Bradley has over 20 years  experience with high content imaging, has worked with many different systems starting with a custom-built, Metamorph journal-run system in the lab of Dr. Steven Finkbeiner. Having overseen high content imaging at companies including Takeda, Arvinas and Cellarity, John was delighted to bring the Endeavor to Ginkgo Bioworks.

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