Very-High-Resolution Time-Lapse Photography for Plant and Ecosystems Research Author(s): Mary H. Nichols, Janet C. Steven, Randy Sargent, Paul Dille, and Joshua Schapiro Source: Applications in Plant Sciences, 1(9) 2013. Published By: Botanical Society of America DOI: http://dx.doi.org/10.3732/apps.1300033 URL: http://www.bioone.org/doi/full/10.3732/apps.1300033
BioOne (www.bioone.org) is a nonprofit, online aggregation of core research in the biological, ecological, and environmental sciences. BioOne provides a sustainable online platform for over 170 journals and books published by nonprofit societies, associations, museums, institutions, and presses. Your use of this PDF, the BioOne Web site, and all posted and associated content indicates your acceptance of BioOne’s Terms of Use, available at www.bioone.org/page/terms_of_use. Usage of BioOne content is strictly limited to personal, educational, and non-commercial use. Commercial inquiries or rights and permissions requests should be directed to the individual publisher as copyright holder.
BioOne sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research libraries, and research funders in the common goal of maximizing access to critical research.
Applications in Plant Sciences 2013 1(9): 1300033
Applications Ap ons
in Pl Plantt Scien Sciences ces
PROTOCOL NOTE
VERY-HIGH-RESOLUTION TIME-LAPSE PHOTOGRAPHY FOR PLANT AND ECOSYSTEMS RESEARCH1
MARY H. NICHOLS2,5, JANET C. STEVEN3, RANDY SARGENT4, PAUL DILLE4, AND JOSHUA SCHAPIRO4 2U.S.
Department of Agriculture–Agricultural Research Service, Southwest Watershed Research Center, 2000 East Allen Road, Tucson, Arizona 85719 USA; 3Department of Biology, Sweet Briar College, 134 Chapel Road, Sweet Briar, Virginia 24595 USA; and 4Robotics Institute, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213 USA
• Premise of the study: Traditional photography is a compromise between image detail and area covered. We report a new method for creating time-lapse sequences of very-high-resolution photographs to produce zoomable images that facilitate observation across a range of spatial and temporal scales. • Methods and Results: A robotic camera mount and software were used to capture images of the growth and movement in Brassica rapa every 15 s in the laboratory. The resultant time-lapse sequence (http://timemachine.gigapan.org/wiki/ Plant_Growth) captures growth detail such as circumnutation. A modified, solar-powered system was deployed at a remote field site in southern Arizona. Images were collected every 2 h over a 3-mo period to capture the response of vegetation to monsoon season rainfall (http://timemachine.gigapan.org/wiki/Arizona_Grasslands). • Conclusions: A technique for observing time sequences of both individual plant and ecosystem response at a range of spatial scales is available for use in the laboratory and in the field. Key words: digital photography; phenology; plant behavior; visualization.
The information contained in traditional single-frame photographs is a compromise between image detail and the amount of area covered. Panoramic tripod mounts can assist with taking sequences of images that can be stitched to produce composite images. A variety of manual and robotic mounts are commercially available. Ongoing advances in technologies for capturing and viewing very-high-resolution images have greatly expanded the capacity to study a broad range of biotic and abiotic ecosystem processes across spatial scales (Sargent et al., 2010a; Brown et al., 2012). The GigaPan system (http:// gigapansystems.com) consists of hardware to capture multiple images on a grid through controlled positioning, software to stitch the images and create very-high-resolution panoramas, and a website to facilitate viewing, searching, exploring, and annotating, and to encourage discussion. Very-high-resolution photography has proven valuable for the study of processes in extreme detail over space in a number of scientific disciplines (Sargent et al., 2010a) including geology, archaeology,
biodiversity, glaciology, and rangeland ecosystem research (Nichols et al., 2009). A logical extension of the ability to capture high-resolution spatial detail is to capture repeat images over time to develop time-lapse sequences. Repeat photography plays an important role in quantitatively assessing changes and processes across many areas of ecosystem research. Examples include landscape change detection and analyses (Turner et al., 2003; Webb et al., 2007; Villarreal et al., 2013) and phenological responses to abiotic drivers (Crimmins and Crimmins, 2008; Richardson et al., 2009; Kurc and Benton, 2010; Sonnentag et al., 2012). Time-lapse imagery is also an important tool in studies of plant behavior (Trewavas, 2009). Time-lapse at the level of a single plant has revealed searching behavior by parasitic plants (Runyon et al., 2006), solar tracking (Hangarter, 2000), and other plant responses to the environment. Typically, only one or a few plants can be captured with a single time-lapse camera at the desired level of detail, limiting sample size and typically confining observations to a laboratory setting. The advantage of imagery captured with the GigaPan system over traditional time-lapse photography is the large increase in resolution over a broader spatial scale, which enables the viewer to make observations both at the level of the individual plant and at the ecosystem level. This increased resolution allows a researcher to capture both variation within a population (Fig. 1) and interactions between the environment and the population within a single sequence, a technique not possible with traditional time-lapse photography. The goals of our project were to produce a very-high-resolution, zoomable, time-lapse video in the laboratory and subsequently to build a reliable, weatherized, solar-powered system for capturing images in the field. Here we describe example
1 Manuscript received 19 April 2013; revision accepted 5 August 2013. The authors thank B. Freniere and the field staff of the Walnut Gulch Experimental Watershed field station whose assistance made this research possible. Funding was provided through the Fine Outreach for Science Fellows Program (http://www.cs.cmu.edu/~fofs/fofs.html). Disclaimer: Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. 5 Author for correspondence: [email protected]
doi:10.3732/apps.1300033
Applications in Plant Sciences 2013 1(9): 1300033; http://www.bioone.org/loi/apps © 2013 Nichols et al. Botanical Society of America. This article is a U.S. Government work and is in the public domain in the USA. 1 of 6
Applications in Plant Sciences 2013 1(9): 1300033 doi:10.3732/apps.1300033
Nichols et al.—Very-High-Resolution Time-Lapse Photography
Fig. 1. Frames from a GigaPan time-lapse sequence of Wisconsin Fast Plants showing (A) the entire group of plants and (B) flowers on three plants. The user can zoom from one level of detail to another while the sequence is running. The full sequence is at http://timemachine.gigapan.org/wiki/ Plant_Growth. http://www.bioone.org/loi/apps
2 of 6
Applications in Plant Sciences 2013 1(9): 1300033 doi:10.3732/apps.1300033
applications showing individual plant growth in a laboratory and landscape-scale vegetation change at a remote rangeland site. Very-high-resolution panoramic photography provides a low-cost (
BioOne (www.bioone.org) is a nonprofit, online aggregation of core research in the biological, ecological, and environmental sciences. BioOne provides a sustainable online platform for over 170 journals and books published by nonprofit societies, associations, museums, institutions, and presses. Your use of this PDF, the BioOne Web site, and all posted and associated content indicates your acceptance of BioOne’s Terms of Use, available at www.bioone.org/page/terms_of_use. Usage of BioOne content is strictly limited to personal, educational, and non-commercial use. Commercial inquiries or rights and permissions requests should be directed to the individual publisher as copyright holder.
BioOne sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research libraries, and research funders in the common goal of maximizing access to critical research.
Applications in Plant Sciences 2013 1(9): 1300033
Applications Ap ons
in Pl Plantt Scien Sciences ces
PROTOCOL NOTE
VERY-HIGH-RESOLUTION TIME-LAPSE PHOTOGRAPHY FOR PLANT AND ECOSYSTEMS RESEARCH1
MARY H. NICHOLS2,5, JANET C. STEVEN3, RANDY SARGENT4, PAUL DILLE4, AND JOSHUA SCHAPIRO4 2U.S.
Department of Agriculture–Agricultural Research Service, Southwest Watershed Research Center, 2000 East Allen Road, Tucson, Arizona 85719 USA; 3Department of Biology, Sweet Briar College, 134 Chapel Road, Sweet Briar, Virginia 24595 USA; and 4Robotics Institute, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213 USA
• Premise of the study: Traditional photography is a compromise between image detail and area covered. We report a new method for creating time-lapse sequences of very-high-resolution photographs to produce zoomable images that facilitate observation across a range of spatial and temporal scales. • Methods and Results: A robotic camera mount and software were used to capture images of the growth and movement in Brassica rapa every 15 s in the laboratory. The resultant time-lapse sequence (http://timemachine.gigapan.org/wiki/ Plant_Growth) captures growth detail such as circumnutation. A modified, solar-powered system was deployed at a remote field site in southern Arizona. Images were collected every 2 h over a 3-mo period to capture the response of vegetation to monsoon season rainfall (http://timemachine.gigapan.org/wiki/Arizona_Grasslands). • Conclusions: A technique for observing time sequences of both individual plant and ecosystem response at a range of spatial scales is available for use in the laboratory and in the field. Key words: digital photography; phenology; plant behavior; visualization.
The information contained in traditional single-frame photographs is a compromise between image detail and the amount of area covered. Panoramic tripod mounts can assist with taking sequences of images that can be stitched to produce composite images. A variety of manual and robotic mounts are commercially available. Ongoing advances in technologies for capturing and viewing very-high-resolution images have greatly expanded the capacity to study a broad range of biotic and abiotic ecosystem processes across spatial scales (Sargent et al., 2010a; Brown et al., 2012). The GigaPan system (http:// gigapansystems.com) consists of hardware to capture multiple images on a grid through controlled positioning, software to stitch the images and create very-high-resolution panoramas, and a website to facilitate viewing, searching, exploring, and annotating, and to encourage discussion. Very-high-resolution photography has proven valuable for the study of processes in extreme detail over space in a number of scientific disciplines (Sargent et al., 2010a) including geology, archaeology,
biodiversity, glaciology, and rangeland ecosystem research (Nichols et al., 2009). A logical extension of the ability to capture high-resolution spatial detail is to capture repeat images over time to develop time-lapse sequences. Repeat photography plays an important role in quantitatively assessing changes and processes across many areas of ecosystem research. Examples include landscape change detection and analyses (Turner et al., 2003; Webb et al., 2007; Villarreal et al., 2013) and phenological responses to abiotic drivers (Crimmins and Crimmins, 2008; Richardson et al., 2009; Kurc and Benton, 2010; Sonnentag et al., 2012). Time-lapse imagery is also an important tool in studies of plant behavior (Trewavas, 2009). Time-lapse at the level of a single plant has revealed searching behavior by parasitic plants (Runyon et al., 2006), solar tracking (Hangarter, 2000), and other plant responses to the environment. Typically, only one or a few plants can be captured with a single time-lapse camera at the desired level of detail, limiting sample size and typically confining observations to a laboratory setting. The advantage of imagery captured with the GigaPan system over traditional time-lapse photography is the large increase in resolution over a broader spatial scale, which enables the viewer to make observations both at the level of the individual plant and at the ecosystem level. This increased resolution allows a researcher to capture both variation within a population (Fig. 1) and interactions between the environment and the population within a single sequence, a technique not possible with traditional time-lapse photography. The goals of our project were to produce a very-high-resolution, zoomable, time-lapse video in the laboratory and subsequently to build a reliable, weatherized, solar-powered system for capturing images in the field. Here we describe example
1 Manuscript received 19 April 2013; revision accepted 5 August 2013. The authors thank B. Freniere and the field staff of the Walnut Gulch Experimental Watershed field station whose assistance made this research possible. Funding was provided through the Fine Outreach for Science Fellows Program (http://www.cs.cmu.edu/~fofs/fofs.html). Disclaimer: Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. 5 Author for correspondence: [email protected]
doi:10.3732/apps.1300033
Applications in Plant Sciences 2013 1(9): 1300033; http://www.bioone.org/loi/apps © 2013 Nichols et al. Botanical Society of America. This article is a U.S. Government work and is in the public domain in the USA. 1 of 6
Applications in Plant Sciences 2013 1(9): 1300033 doi:10.3732/apps.1300033
Nichols et al.—Very-High-Resolution Time-Lapse Photography
Fig. 1. Frames from a GigaPan time-lapse sequence of Wisconsin Fast Plants showing (A) the entire group of plants and (B) flowers on three plants. The user can zoom from one level of detail to another while the sequence is running. The full sequence is at http://timemachine.gigapan.org/wiki/ Plant_Growth. http://www.bioone.org/loi/apps
2 of 6
Applications in Plant Sciences 2013 1(9): 1300033 doi:10.3732/apps.1300033
applications showing individual plant growth in a laboratory and landscape-scale vegetation change at a remote rangeland site. Very-high-resolution panoramic photography provides a low-cost (
