Using Flatbed Scanners to Collect High-resolution Time-lapsed Images of the Arabidopsis Root Gravitropic Response

Smith, Halie C; Niewohner, Devon J; Dewey, Grant D; Longo, Autumn M; Guy, Tracy; Higgins, Bradley R; Daehling, Sarah B; Genrich, Sarah C.; Wentworth, Christopher D.; Brooks, Tessa Durham

doi:10.3791/50878

Cited by 4 publications

(5 citation statements)

References 24 publications

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“…DIAMonDS consists of an automated time-lapse imaging system and our novel image analysis software named ‘Sapphire’ ( Figure 1B ). We used a combination of a flatbed CCD scanner and VueScan software ( https://www.hamrick.com ), which enables multiple scanner units to capture images continuously at certain intervals ( Smith et al, 2014 ). To identify the phase change time points for each fly event, single flies are inserted into each well of a 96- or 384-well microplate containing suitable fly media.…”

Section: Resultsmentioning

confidence: 99%

“…Time-lapse image acquisition To acquire the time-lapse image, we have used a scanner driver, ‘ VueScan ’ (Hamrick Software, USA, https://www.hamrick.com ). The VueScan is able to capture images continuously at several interval timing using multiple units of scanners ( Smith et al, 2014 ). Using the VueScan, we performed time-lapse imaging as following protocol.…”

Section: Fly Media For Diamondsmentioning

confidence: 99%

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The Drosophila Individual Activity Monitoring and Detection System (DIAMonDS)

Seong

Matsumura

Shimada-Niwa

et al. 2020

eLife

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Here, we have developed DIAMonDS (Drosophila Individual Activity Monitoring and Detection System) comprising time-lapse imaging by a charge-coupled device (CCD) flatbed scanner and Sapphire, a novel algorithm and web application. DIAMonDS automatically and sequentially identified the transition time points of multiple life cycle events such as pupariation, eclosion, and death in individual flies at high temporal resolution and on a large scale. DIAMonDS performed simultaneous multiple scans to measure individual deaths (≤1152 flies per scanner) and pupariation and eclosion timings (≤288 flies per scanner) under various chemical exposures, environmental conditions, and genetic backgrounds. DIAMonDS correctly identified 74–85% of the pupariation and eclosion events and ~ 92% of the death events within ± 10 scanning frames. This system is a powerful tool for studying the influences of genetic and environmental factors on fruit flies and efficient, high-throughput genetic and chemical screening in drug discovery.

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Section: Resultsmentioning

confidence: 99%

Section: Fly Media For Diamondsmentioning

confidence: 99%

The Drosophila Individual Activity Monitoring and Detection System (DIAMonDS)

Seong

Matsumura

Shimada-Niwa

et al. 2020

eLife

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show abstract

“…In most systems, the plates have fixed positions [30,47,54]. For imaging, either multiple scanners operate in parallel [1,43,44] or the camera is shifted from one plate to another by using moving stages or a robotic gantry system [30,47,54].…”

Section: Non-destructive Phenotyping Of Root and Shoot Systemsmentioning

confidence: 99%

The platform GrowScreen-Agar enables identification of phenotypic diversity in root and shoot growth traits of agar grown plants

et al. 2020

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Background: Root system architecture and especially its plasticity in acclimation to variable environments play a crucial role in the ability of plants to explore and acquire efficiently soil resources and ensure plant productivity. Nondestructive measurement methods are indispensable to quantify dynamic growth traits. For closing the phenotyping gap, we have developed an automated phenotyping platform, GrowScreen-Agar, for non-destructive characterization of root and shoot traits of plants grown in transparent agar medium. Results: The phenotyping system is capable to phenotype root systems and correlate them to whole plant development of up to 280 Arabidopsis plants within 15 min. The potential of the platform has been demonstrated by quantifying phenotypic differences within 78 Arabidopsis accessions from the 1001 genomes project. The chosen concept 'plant-to-sensor' is based on transporting plants to the imaging position, which allows for flexible experimental size and design. As transporting causes mechanical vibrations of plants, we have validated that daily imaging, and consequently, moving plants has negligible influence on plant development. Plants are cultivated in square Petri dishes modified to allow the shoot to grow in the ambient air while the roots grow inside the Petri dish filled with agar. Because it is common practice in the scientific community to grow Arabidopsis plants completely enclosed in Petri dishes, we compared development of plants that had the shoot inside with that of plants that had the shoot outside the plate. Roots of plants grown completely inside the Petri dish grew 58% slower, produced a 1.8 times higher lateral root density and showed an etiolated shoot whereas plants whose shoot grew outside the plate formed a rosette. In addition, the setup with the shoot growing outside the plate offers the unique option to accurately measure both, leaf and root traits, non-destructively, and treat roots and shoots separately. Conclusions: Because the GrowScreen-Agar system can be moved from one growth chamber to another, plants can be phenotyped under a wide range of environmental conditions including future climate scenarios. In combination with a measurement throughput enabling phenotyping a large set of mutants or accessions, the platform will contribute to the identification of key genes.

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“…To acquire the time-lapse image, we have used a scanner driver, "VueScan" (Hamrick Software, USA, https://www.hamrick.com). The VueScan is able to capture images continuously at several interval timing using multiple units of scanners (Smith et al 2014). Using the VueScan, we performed time-lapse imaging as following protocol.…”

Section: Competing Interestsmentioning

confidence: 99%

TheDrosophilaIndividual Activity Monitoring and Detection System (DIAMonDS)

Seong

Matsumura

Shimada-Niwa

et al. 2020

Preprint

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Here, we have developed DIAMonDS (Drosophila Individual Activity Monitoring and Detection System) comprising time-lapse imaging by a charge-coupled device (CCD) flatbed scanner and Sapphire, a novel algorithm and web application. DIAMonDS automatically and sequentially identified the transition time points of multiple life cycle events such as pupariation, eclosion, and death in individual flies at high temporal resolution and on a large scale. DIAMonDS performed simultaneous multiple scans to measure individual deaths (≤ 1,152 flies per scanner) and pupariation and eclosion timings (≤ 288 flies per scanner) under various chemical exposures, environmental conditions, and genetic backgrounds. DIAMonDS correctly identified 74–85% of the pupariation and eclosion events and ∼92% of the death events within ±10 scanning frames. This system is a powerful tool for studying the influences of genetic and environmental factors on fruit flies and efficient, high-throughput genetic and chemical screening in drug discovery.

show abstract

Using Flatbed Scanners to Collect High-resolution Time-lapsed Images of the Arabidopsis Root Gravitropic Response

Cited by 4 publications

References 24 publications

The Drosophila Individual Activity Monitoring and Detection System (DIAMonDS)

The Drosophila Individual Activity Monitoring and Detection System (DIAMonDS)

The platform GrowScreen-Agar enables identification of phenotypic diversity in root and shoot growth traits of agar grown plants

TheDrosophilaIndividual Activity Monitoring and Detection System (DIAMonDS)

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