Center for High-Throughput
Minimally-Invasive Radiation Biodosimetry

The RABiT Rapid Automated BIodosimetry Tool

P.I. David Brenner, Columbia University


Project 1 is focused on extending the capabilities of the RABiT (Rapid Automated Biodosimetry Tool) Beyond Simple Exposures and Beyond Dose to individual radiosensitiviy.  The RABiT is a fully automated system designed to analyze up to 30,000 samples per day for biodosimetry. The basic system involves two well-characterized assays with all the processing being carried out in-situ in multi-well plates: 1) the g-H2AX assay is a direct measure of the number DNA double strand breaks (DSB) which are present and 2) the micronucleus assay quantifies radiation-induced chromosome damage expressed as post-mitotic micronuclei. Both assays have been shown to be effective in their biodosimetry characteristics and can be used for fast analysis of large populations in the event of a large scale radiological event.

Beyond Simple Exposures moves the RABiT in to the realm of partial body exposures and internal emitters.  The Irradiation Core will handle the exposures of small animals through shielded exposure, organ specific targeted irradiation, and internal emitter exposure.  Calibration of the RABiT assays to distinguish between the characteristics of these types of irradiations will be one focus of Project 1 through.

Beyond Dose focuses on using the host of biodosimetry tools developed for the RABiT verification process to assess inter-individual radiosensitivity on a large scale.  The ability to process up to 30,000 samples per day make it possible to use a large population of animals in initial studies to test the inter-individual radiosensitivity.


RABiT: Rapid Automated High-Throughput Radiation Biodosimetry

The RABiT (Rapid Automated BIodosimetry Tool) is a completely automated, ultra-high throughput robotically-based biodosimetry workstation. It uses advanced, high-speed automated image analysis and robotics to examine tissue samples (e.g., a fingerstick of blood) quickly for quantitative indicators of radiation exposure (e.g., fragments of DNA; DNA repair complexes).

The basic system involves two well-characterized assays with all the processing being carried out in-situ in multi-well plates.

Samples collected within 36 hours of irradiation will be analyzed using the γ-H2AX assay. Following this time, the RABiT will be switched over to micronucleus mode and all subsequent samples analyzed using the micronucleus assay.


Sample collection

We anticipate multiple fingerstick collection sites following a radiological event, such as doctor’s offices, church halls, PoD (Point of Dispensing) sites, hospitals, etc. At these locations, field collection kits, consisting of lancets, bar-coded capillary tubes with matched personal data cards, alcohol wipes, and sample holders for 32 filled capillaries, will be used to collect the samples.


System Layout

Courtesy of Dr. Nathaniel Hupert, MD, MPH at the Weill Cornell Medical College

The robotic biodosimetry workstation consists of four main modules: centrifuge, cell harvesting system, liquid/plate handling robot and dedicated image acquisition/processing system.

A video of the RABiT in action:

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  High-Throughput Imaging Systems for Biodosimetry

Current automated imaging systems have limited throughput, mostly due to their non-specificity. We have therefore built a dedicated high-throughput imaging system for performing the γ-H2AX and micronucleus assays exclusively, seeking creative solutions for rapid sample manipulation, automated focusing and image acquisition and analysis. The throughput of the current imaging system is 6,000 samples per 20-hour day. We are currently under advanced stages of design and component testing to upgrade this system to an anticipated throughput of 5-6 minutes/96-well plate or 20,000-30,000 individual samples/day.


Sample manipulation

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The motion of the sample is separated into two components: a slower coarse motion and a rapid fine motion. The coarse motion is performed by a high speed stage capable of few-g accelerations. This motion is used to move between adjacent samples (9 mm in 50 msec). The fine motion between fields of view within a single sample is performed, not by moving the sample but rather by steering light, using fast galvanometric mirrors as shown right. Typical transit times between adjacent fields of view of the microscope objective are ~1 msec.



A major rate limiting step in an automated imaging system is focusing. Typically, in order to get good image quality, microscope objective lenses have rather small depth of field and are sensitive to the roughness of the sample being imaged. Our solution is to place a weak cylindrical lens in the optics path. Using an appropriately selected lens, a fluorescent bead will be imaged as circular when in focus and as elliptical when out of focus (see movie below), the aspect ratio being proportional to the distance from focus. In the movie the left image shows the resulting ellipse, while the image right shows the object as imaged by regular optics. The object-lens distance can then be corrected in one step.

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Image acquisition and processing

Analysis of the image is performed online, as it is grabbed. By using dichroic mirrors and two cameras, attached to the same frame grabber board we can simultaneously “see” the nucleus and cytoplasm (for the micronucleus assay) or the nucleus and the γ-H2AX fluorescence (for the γ-H2AX assay) and rapidly analyze the images. A third camera, preceded by a cylindrical lens is used for monitoring the focus. The figure above describes the lightpath process. The figures below illustrate the image analysis process for the two different types of assays that can be performed.


Patents Awarded


Zhang J, Salerno A, Simaan N, Yao YL, Randers-Pehrson G, Garty G, Dutta A and Brenner DJ. Systems and methods for robotic transport



Garty G, Brenner DJ, Randers-Pehrson G, Yao YL, Simaan N, Salerno A, Bhatla A, Zhang J, Lyulko OV and Dutta A. Systems and Methods for High-throughput Radiation Biodosimetry



Garty G, Randers-Pehrson G, Brenner DJ and Lyulko OV. Systems and methods for high-speed image scanning



Randers-Pehrson G, Garty G and Brenner DJ. Systems and methods for focusing optics


Provisional Patents

Bhatla A., Salerno A., Simaan N., Yao Y.L., Randers-Pehrson G., Garty G., Brenner D.J. Systems and Methods for Etching Materials. Application Number: 11/895,517

Bhatla A., Brenner D.J., Dutta A., Garty G., Lyulko O.V., Randers-Pehrson G., Salerno A., Simaan N., Yao Y.L., Zhang J. Systems and Methods for High Throughput Radiation Biodosimetry. Application Number: PCT/US07/18931

Bhatla A., Salerno A., Simaan N., Yao Y.L., Randers-Pehrson G., Garty G., Dutta A., Brenner D.J. Systems and Methods for Cutting Materials. Application Number: 11/895,557

Dutta A., Garty G., Randers-Pehrson G., Bhatla A., Salerno A., Simaan N., Yao Y.L., Brenner D.J. Systems and Methods for Radiation Exposure Determination. Application Number: 11/895,361

Randers-Pehrson G., Garty G., Brenner D.J. Systems and Methods for Focusing Optics. Application Number: 11/895,360



Brenner, D.J. Possible high-throughput screening logistics: Integrating high-throughput radiation biodosimetry with high-throughput assays for radiation sensitivity. Radiat. Res. 170:668, 2008. PMCID: PMC3169379. [PDF]

Chen, Y., Zhang, J., Wang, H., Garty, G., Xu, Y., Lyulko, O.V., Turner, H.C., Randers-Pehrson, G., Simaan, N., Yao, Y.L. and Brenner, D.J. Design and preliminary validation of a rapid automated biosodimetry Tool for high througput radiological triage. Proceedings of 2009 ASME/IEEE International Conference on Mechatronic and Embedded Systems and Applications 3:61-67, 2009. PMCID: PMC3024000. [abstract] [PDF]

Chen Y, Wang H, Zhang Jian, Garty G, Simaan N, Yao YL and Brenner DJ. Automated Recognition of Robotic Manipulation Failures in High-throughput Biodosimetry Tool, Expert Systems with Applications, 39:9602-9611 (2012). PMCID: PMC3339769. [abstract]

Garty, G., Chen, Y., Salerno, A., Turner, H., Zhang, J., Lyulko, O.V., Bertucci, A., Xu, Y., Wang, H., Simaan, N., Randers-Pehrson, G., Yao, Y.L., Amundson, S. A. and Brenner D.J. The RABIT: A Rapid Automated Biodosimetry Tool for radiological triage. Health Phys. 98(2):209-217, 2010. PMCID: PMC2923588 [abstract] [PDF]

Garty G, Chen Y, Turner HC. Zhang J, Lyulko O, Bertucci A, Xu Y, Wang H, Simaan N, Randers-Pehrson G, Yao YL, Brenner DJ. The RABIT: A Rapid Automated BIodosimetry Tool For Radiological Triage. II. Technological Developments. International Journal of Radiation Biology, 87:776-790 (2011). PMCID: PMC3176460. [abstract] [PDF]

Garty G, Chen Y, Turner Garty G, Karam A, Brenner DJ. Infrastructure to support ultra high throughput biodosimetry screening after a radiological event. International Journal of Radiation Biology, Aug;87:754-65 (2011). PMCID: PMC3169379. [abstract] [PDF]

Salerno, A., Zhang, J., Bhatla, A., Lyulko, O. V., Nie, J., Dutta, A., Garty, G., Simaan, N., Randers-Pehrson, G., Yao, Y. L. and Brenner, D. J.. "Design Considerations for a Minimally Invasive High-Throughput Automation System for Radiation Biodosimetry". In Proceedings of the Third Annual IEEE Conference on Automation Science and Engineering (CASE), Scottsdale, AZ, September 2007, pp. 846-852. IEEE Catalog Number: 07EX1754C. ISBN: 1-4244-1154-8. Library of Congress: 2007922962. [abstract] [PDF]

Turner HC, Brenner DJ, Chen Y, Bertucci A, Zhang J, Wang H, Lyulko OV, Xu Y, Schaefer J, Simaan N, Randers-Pehrson G, Yao YL, Garty G. Adaptation of the γ-H2AX assay for automated processing in human lymphocytes. Radiation Research, 175:282-290 (2011). PMCID: PMC3121903. [abstract] [PDF]

Xu Y, Garty G, Marino SA, Massey TN, Randers-Pehrson G, Johnson GW and Brenner DJ. Novel neutron sources at the Radiological Research Accelerator Facility, Journal of Instrumentation,7:C03031(2012). PMCID: PMC3337765. [abstract] [PDF]

Chen Y, Zhang J, Wang H, Garty G, Xu Y, Lyulko OV, Turner HC, Randers-Pehrson G, Simaan N, Yao YL and Brenner DJ. Development of a robotically-based automated biodosimetry tool for high-throughput radiological triage. International Journal of Biomechatronics and Biomedical Robotics, 1:115-125; 2010.



Collaborating Institutions

Center for Radiological Research, Columbia University

Department of Mechanical Engineering, Columbia University

National Institutes of Health

City of New York Department of Health and Mental Hygiene

website updated 06/01/2012

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