GigaVision - Quantifying plant life-cycles from organism to ecosystem

Project Overview

The Gigavision camera system enables researchers to study phenology and genomics across entire ecosystems at the scale of individual organisms.

A convergence of recent technological trends is creating an opportunity to transform conventional landscape ecology, phenological (organismal life-cycle) research and science education. Low cost, high performance computers, cheap storage, high throughput genomics, gigapixel resolution camera systems, location-aware smartphones, Web2.0 applications and cloud-based internet computing, provide us with new set off tools with which we can transform traditional landscape ecology, phenological research and science education.

We currently have 3 active cameras. Two are located at our field site in the Indiana Dunes State park (http://gigapan.org/gigapans/43501/, ), and the third unit is located in
Salt Lake City at the University of Utah (http://gigapan.org/gigapans/48031/).

In addition to the camera hardware, we are developing an innovative set of tools for managing, browsing and collecting data from gigapixel
timelapse image sets. An example of the beta timelapse player is below.

Project Overview

We recently finished up an invited chapter on the Gigavision Project for a book on High Throughput Phenotyping in Plants. Check it out if you are interested in a detailed review of the technology behind the Gigavision system. We'd also love to hear from you if you have any questions or ideas. Contact us here.

Gigavision Cameras

Gigapixel Timelapse Player - Big Blowout East (BBE) Site

View 80MP Live Feed (click)

Interactive timelapse player with plant data layer enabled:

Other ways to view the data: [View 80MP Live Feed (no phenology data)] [View Full Screen]  [View with Phenology data][BBE Main Project Page]

Salt Lake City 360 Degree Meterology Camera

Gigavision camera system details:

• Solar powered camera system
  
• Captures a 1-5 billion pixel image every hour in a 350 degree panorama.
• Images can be transmitted wirelessly to the remote stitching server and browsable online within an hour of capture.
• Record life-cycle (phenology) data from nearly every plan in the landscape.
• Image and phenology data is available online in an interactive interface layering plant-level phenology data with gigapixel resolution images, genomic sequence data from individual plants and with weather and other abitotic sensor data.

GIGAVISION - DEMO MOVIE

Gigavision demo video (rough draft) from TimeScience on Vimeo.

More information

Stitching software

All of our timelapse gigapixel panoramas are stitched using the stitching software available from gigapan. The entire process is automated usiong custom developed script.

For hand shot panoramas, we also use autopano giga pro

Stitcher Status

Embedding in google earth

Gigapixel images on the gigapan.org site can be embeded in Google Earth (for example: kml)

Course work

Prairieecosystems class assignments

Data Availability

We expect to share several Tb of GigaVision through a local server.

Background

Prior to developing the automated gigavision system We used the gigapan.org panoramic tripod mount and canon powershot SX10IS camera to take sand dune blowout ecosystem panoramics at almost weekly intervals through 2009. 

We will continue to shoot multiple gigapans in the field on a weekly basis and we plan to install additional automatic Gigavision cameras in the field as resources permit. The Gigavision system increase our sample rate to hourly intervals through the growing season. The high resolution (~ 32Gb memory card swapped weekly) will allow plant level zoom and play. Thumbnails are being transmitted the stitched in real time for habitat level observations.

Gigavision hardware

System description

Gigavision is a hardware/software system that enables recording and analysis of decades-long time‑lapse images of the environment at a scale of billions of pixels. Gigapixel resolution time-lapse images make possible visual and numeric analysis of phenological and environmental change across a wide spatial range from the level of the individual to the ecosystem. Gigavision data can be embedded in geospatial visualization tools such as Google Earth and Google maps and used in interactive kiosk displays in National Parks and conservation areas. In addition to scientific applications, gigapixel time-lapse datasets can be used to create compelling video content to promote conservation and educate the public about climate change and other slow but significant environmental change. Gigapixel image sets can also be integrated into online interactive educational products.

The Gigavision system consists of a recording and playback system that work together seamlessly. The primary goal in system design is to maximize ease of use both in deployment of the recording system and in analysis and visualization of the recorded data. A core design principle for the TimeSystem playback system is to maximize standardization in a way that facilitates the widest possible range of uses for the recorded data.

The Gigavision recording system uses a standard 10 megapixel SLR digital camera, a computer controlled pan-tilt mechanism, a mini-computer or microcontroller, solid state data storage, a weatherproof housing and an off-grid power supply. Gigavision systems will be designed to work in rugged environments while streaming live data directly to the web via a cellular or standard 802.11 wireless connection. Optional components include weather sensors and other abiotic sensor arrays.

The Gigavision recording system will be developed to work with the TimeSystem software package created by TimeScience. The TimeSystem software is an innovative data visualization system designed to facilitate easy analysis and management of time-lapse images and related data. With both a desktop and web-based interface, TimeSystem enables easy sharing of data, collaboration between researchers and promotes a wide range of uses for long-term data sets, from academic research to educational modules. The TimeSystem interface is easily configured for use by a range of user groups from research scientists, to educators, to conservation groups. The TimeSystem software allows users to quickly create high definition video of landscape change or any other interesting event for presentations, public outreach or conservation campaigns. The TimeSystem can also function in a kiosk installation to provide compelling interactive time-lapse content for National Parks and conservation areas.

How it works

The Gigavision recording system consists of a stock 10 megapixel SLR digital camera with a 100–200mm zoom lens, a computer controlled pan-tilt mechanism, a netbook mini-computer or microcontroller, a weatherproof housing and an off-grid power supply. Optional components include a weather system and other abiotic sensor arrays, wireless connectivity (either via the cellular GSRM network or standard 802.11 internet wireless).

Each gigapixel image is created by shooting a panorama consisting of 200 – 300 overlapping 10 megapixel images taken over a 5-10 minute period. Individually, each image captures a high resolution snapshot of a tiny portion of the total view; when stitched together, these images create a 1-2 billion pixel image of a 180 degree view of the landscape.

The camera and pan-tilt unit are controlled with custom-designed software running on a pc or microcontroller. For each snapshot in the full panorama, the computer sets the camera position with the pan-tilt unit, snaps a photo and downloads the image to the hard drive. If the system is enabled for wireless internet access, the computer then uploads all the images to the Gigavision server where the individual images are processed into a full panorama.

TimeSystem playback system for Gigavision images

Desktop version
The desktop application is a windows-based playback system that provides the user with an intuitive interface for watching the entire timelapse at any playback rate. Mouse-based controls let users zoom into any point within the larger panorama as well as to quickly review any time period from a few hours to years or decades. The TimeSystem software provides zoom and panning functionality as well as bookmarking and annotation tools. Users can also export a movie of any part of the timelapse at any zoom level. The movie export tools allow users to quickly generate compelling content for presentations or web playback. Advanced system functionalities include graphing components for co-visualizing any time-based numeric data set such as weather or climatic data along with the gigapixel time-lapse images.

In addition to research applications, Gigvision imagesets provide an exceptional opportunity for creating unique educational displays for museums, national parks and tourist destination. A TimeSystem kiosk installation consists of a playback computer, a large LCD display and a controller. The kiosk interface consists of a large arcade-style spinning dial for moving through time and a joystick for zooming and panning in the images. Future version could have an interface similar to the telescopes common at tourist sites. Just as with a regular mounted telescope, the user could zoom and pan around within the view, however the TimeSystem-enabled telescope would show either the live image or recorded images from the timelapse, allowing the user to look back in time while they zoomed and panned within the view the were exploring. TimeSystem kiosk systems could play back image streams from both on-site camera systems as well as any remote camera with the images downloaded via the internet. In a National Park or other conservation setting, a TimeSystem kiosk would provide resource managers with a compelling, interactive tool to showcase environmental change, restoration efforts, etc.

Online version

Online visualization of Gigavision data consists of a Flash-based playback system similar to the desktop version. Initial functionality will mimic the desktop version to the greatest extent possible within the constraints of existing bandwidth and processor limitations. The online Gigavision system will provide user accounts so individuals can customize data views and data sets and share data within collaborative groups, etc. Online tools will include bookmarking and the ability to export or download, movies, subsets of data and individual images, etc. A web-based interface also permits additional collaborative, social-networking and educational functionalities not possible in the desktop version. For example, the online interface can provide user accounts for different user groups such as “researcher”, “educator”, “student”, etc. For each group or individual, the site administrator will be able to select what datasets are available. Each user group will also have sets of tools aimed for their primary needs.  For example researchers might have collaborative tools geared towards collaboration and publication of results. Educators could have tools to create a constrained dataset more appropriate to a certain grade level and students users could have tools for writing reports and working on projects as a group.

Project Contacts and Hardware