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Networks, pixels and smart devices
Next gen ecology in a changing world
Tim Brown, Postdoctoral Fellow
Research school of ...
More than 7 billion people on the planet for the next 100 years
(Figure: Ezeh et al. The Lancet - 14 July 2012
At the same time the global climate will warm by 3-6° C
• This will greatly increase variability and severity of weather e...
Global climate will warm by 4-6° C by 2100
• 53% of Eucalyptus species will be out of their native ranges1
(Google Maps )
...
If we believe what the science is telling us
the next century will not be a pleasant one.
The question is no longer “How d...
If we believe what the science is telling us
the next century will not be a pleasant one.
The question is no longer “How d...
If we believe what the science is telling us
the next century will not be a pleasant one.
The question is no longer “How d...
If we believe what the science is telling us
the next century will not be a pleasant one.
The question is no longer “How d...
If we believe what the science is telling us
the next century will not be a pleasant one.
The question is no longer “How d...
Genotype x Environment = Phenotype
Phenotype (and ecosystem function) emerges as a cross-
scale interaction between genoty...
Genotype x Environment = Phenotype
Phenotype (and ecosystem function) emerges as a cross-
scale interaction between genoty...
Genotype x Environment = Phenotype
Phenotype (and ecosystem function) emerges as a cross-
scale interaction between genoty...
Genotype x Environment = Phenotype
Phenotype (and ecosystem function) emerges as a cross-
scale interaction between genoty...
Genotype x Environment = Phenotype
Phenotype (and ecosystem function) emerges as a cross-
scale interaction between genoty...
Current Work
How do we capture what is going on in the
environment, quantify it and provide it to scientists
(and the publ...
Current Work
How do we capture what is going on in the environment,
quantify it and provide it to scientists (and the publ...
Current Work
How do we capture what is going on in the environment,
quantify it and provide it to scientists (and the publ...
Current Work
How do we capture what is going on in the environment,
quantify it and provide it to scientists (and the publ...
Current Work
How do we capture what is going on in the environment,
quantify it and provide it to scientists (and the publ...
Lab phenotyping
High precision measurements but low realism
In the lab we can control environment and measure phenotype wi...
Field phenotyping
Realistic environment but low precision measurements
In the field we have real environments but the comp...
NextGen Ecology – Where’s my PCR?
• Ecology is like genetics before PCR and high throughput sequencing
• Remember back in ...
NextGen Ecology – Where’s my PCR?
• Ecology is like genetics before PCR and high throughput sequencing
• Remember back in ...
Genetics -> Genomics -> Phenomics
20 years of technical advances have turned genetics into genomics into
phenomics and yie...
Genetics -> Genomics -> Phenomics
20 years of technical advances have turned genetics into genomics into
phenomics and yie...
Genetics -> Genomics -> Phenomics
20 years of technical advances have turned genetics into genomics into
phenomics and yie...
Genetics -> Genomics -> Phenomics
20 years of technical advances have turned genetics into genomics into
phenomics and yie...
Genetics -> Genomics -> Phenomics
20 years of technical advances have turned genetics into genomics into
phenomics and yie...
Genetics -> Genomics -> Phenomics
20 years of technical advances have turned genetics into genomics into
phenomics and yie...
Genetics -> Genomics -> Phenomics
20 years of technical advances have turned genetics into genomics into
phenomics and yie...
TERN will be a multi-decade project
NEON is 30-year project
• 30 years ago was ~1980 (everything was analog)
New technolog...
TERN will be a multi-decade project
NEON is 30-year project
• 30 years ago was ~1980 (everything was analog)
– The first s...
TERN will be a multi-decade project
NEON is 30-year project
• 30 years ago was ~1980 (everything was analog)
– The first s...
TERN will be a multi-decade project
NEON is 30-year project
• 30 years ago was ~1980 (everything was analog)
– The first s...
Current capacity is very limited in most field work
“Typical” field site:
• One weather station (temp, humidity, rain
gaug...
Current capacity is very limited in most field work
“Typical” field site:
• One weather station (temp, humidity, rain
gaug...
Current capacity is very limited in most field work
“Typical” field site:
• One weather station (temp, humidity, rain
gaug...
Field site of the future…
Within 10 years we could have:
Field site of the future…
Within 10 years we could have:
• Time-series 3D model of every field site
Field site of the future…
Within 10 years we could have:
• Time-series 3D model of every field site
• Daily hyperspectral ...
Field site of the future…
Within 10 years we could have:
• Time-series 3D model of every field site
• Daily hyperspectral ...
Field site of the future…
Within 10 years we could have:
• Time-series 3D model of every field site
• Daily hyperspectral ...
Field site of the future…
Within 10 years we could have:
• Time-series 3D model of every field site
• Daily hyperspectral ...
Field site of the future…
Within 10 years we could have:
• Time-series 3D model of every field site
• Daily hyperspectral ...
Field site of the future…
Within 10 years we could have:
• Time-series 3D model of every field site
• Daily hyperspectral ...
Field site of the future…
Within 10 years we could have:
• Time-series 3D model of every field site
• Daily hyperspectral ...
Gigapixel Imaging
Gigapixel Imaging
-
Golfer, 7km distant
(Single 15MP image)
Area: ~7ha
Area: ~1m2
The Gigapan and
Gigavision systems
allow you to capture
hundreds or
thousands of...
Gigavision: Gigapixel time-lapse camera
• 2008 - TimeScience (my company) & U Chicago (Borevitz Lab)
• Capture timelapse o...
Gigavision: Gigapixel time-lapse camera
• 2008 - TimeScience (my company) & U Chicago (Borevitz Lab)
• Capture timelapse o...
Gigavision: Gigapixel time-lapse camera
• 2008 - TimeScience (my company) & U Chicago (Borevitz Lab)
• Capture timelapse o...
Unmanned Aerial Systems (UAV/UAS)
• Tech is very new
– Getting much easier & cheaper VERY quickly
• Current regs are restr...
Unmanned Aerial Systems (UAV/UAS)
• Tech is very new
– Getting much easier & cheaper VERY quickly
• Current regs are restr...
3D Reconstruction from UAV images
• 5cm resolution 3D point cloud from UAV images
(DEM/orthorectified, etc).
– Software Co...
http://www.youtube.com/watch?v=-11Sb531lPs
Building a 6mm resolution 3D mesh from UAV images
Sequencing and microclimate sensors
Sequencing:
• Reduced representation plant genome sequence costs < $50/ plant
– Should...
Sequencing and microclimate sensors
Sequencing:
• Reduced representation plant genome sequence costs < $50/ plant
– Should...
Sequencing and microclimate sensors
Sequencing:
• Reduced representation plant genome sequence costs < $50/ plant
– Should...
Developing an International Phenocam Network
Everyone is installing cameras now because they
are cheap
Cheap IP cameras on...
Developing an International Phenocam Network
Everyone is installing cameras now because they
are cheap
The challenge:
• Ge...
Developing an International Phenocam Network
Everyone is installing cameras now because they
are cheap
The challenge:
• Ge...
Developing an International Phenocam Network
Everyone is installing cameras now because they
are cheap
The challenge:
• Ge...
Developing an International Phenocam Network
Everyone is installing cameras now because they
are cheap
The challenge:
• Ge...
TERN is uniquely suited to help facilitate an international phenocam network
TERN can lead in:
• Collecting long-term data...
TERN is uniquely suited to help facilitate an international phenocam network
TERN can lead in:
• Collecting long-term data...
TERN is uniquely suited to help facilitate an international phenocam network
TERN can lead in:
• Collecting long-term data...
TERN is uniquely suited to help facilitate an international phenocam network
TERN can lead in:
• Collecting long-term data...
Enabling Phenocam networks: How do we get everyone on board?
• Reduce barriers to participation at all levels
– Google met...
Enabling Phenocam networks: How do we get everyone on board?
• Reduce barriers to participation at all levels
– Google met...
Enabling Phenocam networks: How do we get everyone on board?
• Reduce barriers to participation at all levels
– Google met...
Enabling Phenocam networks: How do we get everyone on board?
• Reduce barriers to participation at all levels
– Google met...
Let’s build a phenocam network where it takes 1 minute to sign up
Let’s build a phenocam network where it takes 1 minute to sign up
Let’s build a phenocam network where it takes 1 minute to sign up
Let’s build a phenocam network where it takes 1 minute to sign up
• Archives are automatically and stored in
permanent arc...
Let’s build a phenocam network where it takes 1 minute to sign up
• Archives are automatically and stored in
permanent arc...
http://www.uvu.edu/crfs/livefeed/http://phenocam.sr.unh.edu/webcam/sites/bartlettir/
Data/Image visualization
http://www.d...
Final questions
• I always focus on things from a “capacity” perspective
because I think more data is always better so Whe...
Final questions
• I always focus on things from a “capacity” perspective
because I think more data is always better so Whe...
Final questions
• I always focus on things from a “capacity” perspective
because I think more data is always better so Whe...
Final questions
• I always focus on things from a “capacity” perspective
because I think more data is always better so Whe...
Final questions
• I always focus on things from a “capacity” perspective
because I think more data is always better so Whe...
The pace of change is accelerating
Panono (panono.com)
• 108MP instant panoramas
• $600AUD
• Indiegogo: $1.2 M USD
Oculus ...
media.pixelcase.com/360video/huntervalley/index.html
How do we process all this stuff?!
• In < 5 years Google has created 360 deg panoramas of 5 million
miles of streets (20 p...
Credits & Thanks
Justin Borevitz and the Borevitz Lab, ANU
borevitzlab.anu.edu.au
Gigavision Camera Project
Justin Borevit...
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Tim Brown ACEAS Phenocams

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Pixels, networks and smart data: next gen ecology in a changing world

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Tim Brown ACEAS Phenocams

  1. 1. Networks, pixels and smart devices Next gen ecology in a changing world Tim Brown, Postdoctoral Fellow Research school of biology Australian National University
  2. 2. More than 7 billion people on the planet for the next 100 years (Figure: Ezeh et al. The Lancet - 14 July 2012
  3. 3. At the same time the global climate will warm by 3-6° C • This will greatly increase variability and severity of weather events • Growing regions will probably shift by 600 – 900 km (150Km/°C) • We will need to produce 70% more food by 2050 to feed all these people1 Figure: Moritz & Agudo. 2013. Science 341 (6145), 504-508 1) Tester & LeGrange. 2010. Science:327(818)
  4. 4. Global climate will warm by 4-6° C by 2100 • 53% of Eucalyptus species will be out of their native ranges1 (Google Maps ) 1) Hughes et al. Climatic range sizes of Eucalyptus species in relation to future climate change. Global Ecology and Biogeography Letters (1996): 23-29.
  5. 5. If we believe what the science is telling us the next century will not be a pleasant one. The question is no longer “How do we prevent this?” it is: “How do we minimize how bad things will get?”
  6. 6. If we believe what the science is telling us the next century will not be a pleasant one. The question is no longer “How do we prevent this?” it is: “How do we minimize how bad things will get?” We no longer have the luxury of using low resolution ecological models
  7. 7. If we believe what the science is telling us the next century will not be a pleasant one. The question is no longer “How do we prevent this?” it is: “How do we minimize how bad things will get?” We no longer have the luxury of using low resolution ecological models We need to be tracking “everything” in the environment at high frequency for long periods of time.
  8. 8. If we believe what the science is telling us the next century will not be a pleasant one. The question is no longer “How do we prevent this?” it is: “How do we minimize how bad things will get?” We no longer have the luxury of using low resolution ecological models We need to be tracking “everything” in the environment at high frequency for long periods of time. TERN/ACEAS is uniquely positioned to facilitate this: – Establishing long term continent-wide monitoring – Pave the way for collaborative use of big data – Data standards!
  9. 9. If we believe what the science is telling us the next century will not be a pleasant one. The question is no longer “How do we prevent this?” it is: “How do we minimize how bad things will get?” We no longer have the luxury of using low resolution ecological models We need to be tracking “everything” in the environment at high frequency for long periods of time. TERN/ACEAS is uniquely positioned to facilitate this: – Establishing long term continent-wide monitoring – Pave the way for collaborative use of big data – Data standards! Near-surface remote sensing can vastly increase the temporal and spatial resolution of available environmental data.
  10. 10. Genotype x Environment = Phenotype Phenotype (and ecosystem function) emerges as a cross- scale interaction between genotypes and their environment
  11. 11. Genotype x Environment = Phenotype Phenotype (and ecosystem function) emerges as a cross- scale interaction between genotypes and their environment The degree to which we can measure G, E, P is the degree to which we can understand ecosystem function
  12. 12. Genotype x Environment = Phenotype Phenotype (and ecosystem function) emerges as a cross- scale interaction between genotypes and their environment The degree to which we can measure G, E, P is the degree to which we can understand ecosystem function • Phenomics lets us we split out – Traits – the genetically heritable component of phenotype – Plasticity – the environmental component phenotype
  13. 13. Genotype x Environment = Phenotype Phenotype (and ecosystem function) emerges as a cross- scale interaction between genotypes and their environment The degree to which we can measure G, E, P is the degree to which we can understand ecosystem function • Phenomics lets us we split out – Traits – the genetically heritable component of phenotype – Plasticity – the environmental component phenotype • What is the scale and rate of local adaptation?
  14. 14. Genotype x Environment = Phenotype Phenotype (and ecosystem function) emerges as a cross- scale interaction between genotypes and their environment The degree to which we can measure G, E, P is the degree to which we can understand ecosystem function • Phenomics lets us we split out – Traits – the genetically heritable component of phenotype – Plasticity – the environmental component phenotype • What is the scale and rate of local adaptation? • GxE=P lets us predict climate change impacts – How “brittle” are specific ecosystems?
  15. 15. Current Work How do we capture what is going on in the environment, quantify it and provide it to scientists (and the public) in a format that they can use?
  16. 16. Current Work How do we capture what is going on in the environment, quantify it and provide it to scientists (and the public) in a format that they can use? (1) Lab phenomics – Identifying the genetic basis of plant growth and development
  17. 17. Current Work How do we capture what is going on in the environment, quantify it and provide it to scientists (and the public) in a format that they can use? (1) Lab phenomics – Identifying the genetic basis of plant growth and development (2) Field ecology – High resolution monitoring of ecosystems
  18. 18. Current Work How do we capture what is going on in the environment, quantify it and provide it to scientists (and the public) in a format that they can use? (1) Lab phenomics – Identifying the genetic basis of plant growth and development (2) Field ecology – High resolution monitoring of ecosystems
  19. 19. Current Work How do we capture what is going on in the environment, quantify it and provide it to scientists (and the public) in a format that they can use? (1) Lab phenomics – Identifying the genetic basis of plant growth and development (2) Field ecology – High resolution monitoring of ecosystems How do we phenotype thousands of plants at high spatial and temporal resolution at low cost.
  20. 20. Lab phenotyping High precision measurements but low realism In the lab we can control environment and measure phenotype with high precision And we have to develop data pipelines to phenotype 2-3,000 plants continuously
  21. 21. Field phenotyping Realistic environment but low precision measurements In the field we have real environments but the complexity (and bad lighting!) reduces our ability to measure things with precision
  22. 22. NextGen Ecology – Where’s my PCR? • Ecology is like genetics before PCR and high throughput sequencing • Remember back in the ’80s & early 90s when people would get a PhD just sequencing a single gene?
  23. 23. NextGen Ecology – Where’s my PCR? • Ecology is like genetics before PCR and high throughput sequencing • Remember back in the ’80s & early 90s when people would get a PhD just sequencing a single gene? • Humane Genome Project cost $2.7billion USD and took 13 years • Now (20 years in) we buy sequencing machines on ebay and light sequence whole genomes for <$50 a plant in just a few weeks
  24. 24. Genetics -> Genomics -> Phenomics 20 years of technical advances have turned genetics into genomics into phenomics and yielded the ability to address fundamental and very complex questions
  25. 25. Genetics -> Genomics -> Phenomics 20 years of technical advances have turned genetics into genomics into phenomics and yielded the ability to address fundamental and very complex questions Now state of the art phenomics is almost able to track “everything all the time” • CSIRO High Resolution Plant Phenomics Center Glasshouse Capacity: – Time-series hyperspectral and 3D imaging including Thermal & LIDAR
  26. 26. Genetics -> Genomics -> Phenomics 20 years of technical advances have turned genetics into genomics into phenomics and yielded the ability to address fundamental and very complex questions Now state of the art phenomics is almost able to track “everything all the time” • CSIRO High Resolution Plant Phenomics Center Glasshouse Capacity: – Time-series hyperspectral and 3D imaging including Thermal & LIDAR – Generates: • 3D time-lapse models of every plant growing with each pixel in all spectra mapped to the 3D “data cube” model of each plant
  27. 27. Genetics -> Genomics -> Phenomics 20 years of technical advances have turned genetics into genomics into phenomics and yielded the ability to address fundamental and very complex questions Now state of the art phenomics is almost able to track “everything all the time” • CSIRO High Resolution Plant Phenomics Center Glasshouse Capacity: – Time-series hyperspectral and 3D imaging including Thermal & LIDAR – Generates: • 3D time-lapse models of every plant growing with each pixel in all spectra mapped to the 3D “data cube” model of each plant – Precision environmental controls
  28. 28. Genetics -> Genomics -> Phenomics 20 years of technical advances have turned genetics into genomics into phenomics and yielded the ability to address fundamental and very complex questions Now state of the art phenomics is almost able to track “everything all the time” • CSIRO High Resolution Plant Phenomics Center Glasshouse Capacity: – Time-series hyperspectral and 3D imaging including Thermal & LIDAR – Generates: • 3D time-lapse models of every plant growing with each pixel in all spectra mapped to the 3D “data cube” model of each plant – Precision environmental controls – Genome sequence for every plant
  29. 29. Genetics -> Genomics -> Phenomics 20 years of technical advances have turned genetics into genomics into phenomics and yielded the ability to address fundamental and very complex questions Now state of the art phenomics is almost able to track “everything all the time” • CSIRO High Resolution Plant Phenomics Center Glasshouse Capacity: – Time-series hyperspectral and 3D imaging including Thermal & LIDAR – Generates: • 3D time-lapse models of every plant growing with each pixel in all spectra mapped to the 3D “data cube” model of each plant – Precision environmental controls – Genome sequence for every plant – Automated bioinformatics pipeline for trait extraction
  30. 30. Genetics -> Genomics -> Phenomics 20 years of technical advances have turned genetics into genomics into phenomics and yielded the ability to address fundamental and very complex questions Now state of the art phenomics is almost able to track “everything all the time” • CSIRO High Resolution Plant Phenomics Center Glasshouse Capacity: – Time-series hyperspectral and 3D imaging including Thermal & LIDAR – Generates: • 3D time-lapse models of every plant growing with each pixel in all spectra mapped to the 3D “data cube” model of each plant – Precision environmental controls – Genome sequence for every plant – Automated bioinformatics pipeline for trait extraction But ecosystems are more complex than plants in growth chambers… We need significantly higher resolution capacity in the field
  31. 31. TERN will be a multi-decade project NEON is 30-year project • 30 years ago was ~1980 (everything was analog) New technology will enable NextGen ecology too 1.http://www.popsci.com/node/31716 2.http://modis.gsfc.nasa.gov/about/specifications.php 3.https://www.lte.vzw.com/AboutLTE/VerizonWirelessLTENetwork/tabid/6003/Default.aspx
  32. 32. TERN will be a multi-decade project NEON is 30-year project • 30 years ago was ~1980 (everything was analog) – The first space shuttle (1981) 1MB of RAM1 (your phone has 1000x this) New technology will enable NextGen ecology too 1.http://www.popsci.com/node/31716 2.http://modis.gsfc.nasa.gov/about/specifications.php 3.https://www.lte.vzw.com/AboutLTE/VerizonWirelessLTENetwork/tabid/6003/Default.aspx
  33. 33. TERN will be a multi-decade project NEON is 30-year project • 30 years ago was ~1980 (everything was analog) – The first space shuttle (1981) 1MB of RAM1 (your phone has 1000x this) – 4G is the same bandwidth that MODIS uses to download a full satellite image of the earth every day (MODIS: 6.1Mbps avg; Verizon 4G: 5-12Mbps 2,3) New technology will enable NextGen ecology too 1.http://www.popsci.com/node/31716 2.http://modis.gsfc.nasa.gov/about/specifications.php 3.https://www.lte.vzw.com/AboutLTE/VerizonWirelessLTENetwork/tabid/6003/Default.aspx
  34. 34. TERN will be a multi-decade project NEON is 30-year project • 30 years ago was ~1980 (everything was analog) – The first space shuttle (1981) 1MB of RAM1 (your phone has 1000x this) – 4G is the same bandwidth that MODIS uses to download a full satellite image of the earth every day (MODIS: 6.1Mbps avg; Verizon 4G: 5-12Mbps 2,3) • When our kids grow up, what datasets can we have ready for them to use? New technology will enable NextGen ecology too 1.http://www.popsci.com/node/31716 2.http://modis.gsfc.nasa.gov/about/specifications.php 3.https://www.lte.vzw.com/AboutLTE/VerizonWirelessLTENetwork/tabid/6003/Default.aspx
  35. 35. Current capacity is very limited in most field work “Typical” field site: • One weather station (temp, humidity, rain gauge, maybe soil moisture, sunlight)
  36. 36. Current capacity is very limited in most field work “Typical” field site: • One weather station (temp, humidity, rain gauge, maybe soil moisture, sunlight) • Much work is manual: hand measurements, subjective observations, etc. – Manual measurements are often only for short time periods (e.g. 1-2 yrs) – Repeat experiments to verify results are often at a different site by different observers
  37. 37. Current capacity is very limited in most field work “Typical” field site: • One weather station (temp, humidity, rain gauge, maybe soil moisture, sunlight) • Much work is manual: hand measurements, subjective observations, etc. – Manual measurements are often only for short time periods (e.g. 1-2 yrs) – Repeat experiments to verify results are often at a different site by different observers • Some more advanced long term sites (e.g. TERN, NEON, fluxnet), but little phenotyping
  38. 38. Field site of the future… Within 10 years we could have:
  39. 39. Field site of the future… Within 10 years we could have: • Time-series 3D model of every field site
  40. 40. Field site of the future… Within 10 years we could have: • Time-series 3D model of every field site • Daily hyperspectral and thermal data layered over every plant with cm accuracy
  41. 41. Field site of the future… Within 10 years we could have: • Time-series 3D model of every field site • Daily hyperspectral and thermal data layered over every plant with cm accuracy • Every long lived species is sequenced so population genetics is known
  42. 42. Field site of the future… Within 10 years we could have: • Time-series 3D model of every field site • Daily hyperspectral and thermal data layered over every plant with cm accuracy • Every long lived species is sequenced so population genetics is known • Microclimate mesh sensor networks provide growth and environmental data for every tree
  43. 43. Field site of the future… Within 10 years we could have: • Time-series 3D model of every field site • Daily hyperspectral and thermal data layered over every plant with cm accuracy • Every long lived species is sequenced so population genetics is known • Microclimate mesh sensor networks provide growth and environmental data for every tree • Advanced visualization tools let you fly into any site to look around, grab data from any location – Slide back in time and watch any interaction for as long as there have been sensors – Query field sites globally for matching or contrasting environments with the same data and all genetics available – Back-end bioinformatics pipelines for automated data mining (cloud computing solutions) – Generate snapshot and comparisons of data on the fly to share with colleagues
  44. 44. Field site of the future… Within 10 years we could have: • Time-series 3D model of every field site • Daily hyperspectral and thermal data layered over every plant with cm accuracy • Every long lived species is sequenced so population genetics is known • Microclimate mesh sensor networks provide growth and environmental data for every tree • Advanced visualization tools let you fly into any site to look around, grab data from any location – Slide back in time and watch any interaction for as long as there have been sensors – Query field sites globally for matching or contrasting environments with the same data and all genetics available – Back-end bioinformatics pipelines for automated data mining (cloud computing solutions) – Generate snapshot and comparisons of data on the fly to share with colleagues • Start new research projects beginning with all the data previously collected at a site
  45. 45. Field site of the future… Within 10 years we could have: • Time-series 3D model of every field site • Daily hyperspectral and thermal data layered over every plant with cm accuracy • Every long lived species is sequenced so population genetics is known • Microclimate mesh sensor networks provide growth and environmental data for every tree • Advanced visualization tools let you fly into any site to look around, grab data from any location – Slide back in time and watch any interaction for as long as there have been sensors – Query field sites globally for matching or contrasting environments with the same data and all genetics available – Back-end bioinformatics pipelines for automated data mining (cloud computing solutions) – Generate snapshot and comparisons of data on the fly to share with colleagues • Start new research projects beginning with all the data previously collected at a site • In the field tablets, Google glass or similar augmented reality tools let you view high precision data mapped onto the actual plants you are looking at
  46. 46. Field site of the future… Within 10 years we could have: • Time-series 3D model of every field site • Daily hyperspectral and thermal data layered over every plant with cm accuracy • Every long lived species is sequenced so population genetics is known • Microclimate mesh sensor networks provide growth and environmental data for every tree • Advanced visualization tools let you fly into any site to look around, grab data from any location – Slide back in time and watch any interaction for as long as there have been sensors – Query field sites globally for matching or contrasting environments with the same data and all genetics available – Back-end bioinformatics pipelines for automated data mining (cloud computing solutions) – Generate snapshot and comparisons of data on the fly to share with colleagues • Start new research projects beginning with all the data previously collected at a site • In the field tablets, Google glass or similar augmented reality tools let you view high precision data mapped onto the actual plants you are looking at So how do we do this?
  47. 47. Gigapixel Imaging
  48. 48. Gigapixel Imaging - Golfer, 7km distant
  49. 49. (Single 15MP image) Area: ~7ha Area: ~1m2 The Gigapan and Gigavision systems allow you to capture hundreds or thousands of zoomed-in images in a panorama. Images are then “Stitched” into a seamless panorama. The super-high resolution of the final panorama lets you monitor huge landscape areas in great detail. Gigapixel Imaging – How it works
  50. 50. Gigavision: Gigapixel time-lapse camera • 2008 - TimeScience (my company) & U Chicago (Borevitz Lab) • Capture timelapse of every leaf on every tree within a few hectares
  51. 51. Gigavision: Gigapixel time-lapse camera • 2008 - TimeScience (my company) & U Chicago (Borevitz Lab) • Capture timelapse of every leaf on every tree within a few hectares • ~1-2 billion pixels / panorama = Avg. resolution of ~1-2 pixel / cm over 7 hectares – (~600 million > MODIS resolution) • Solar powered; wireless/cellular • Data management and extraction are a challenge
  52. 52. Gigavision: Gigapixel time-lapse camera • 2008 - TimeScience (my company) & U Chicago (Borevitz Lab) • Capture timelapse of every leaf on every tree within a few hectares • ~1-2 billion pixels / panorama = Avg. resolution of ~1-2 pixel / cm over 7 hectares – (~600 million > MODIS resolution) • Solar powered; wireless/cellular • Data management and extraction are a challenge The Future • Standardized control software (AXIS VAPIX protocols and PelcoD) would enable almost ANY cheap PTZ camera to become a gigapixel timelapse camera • Cloud solution for data processing -> Just buy a camera and plug it in and post- processing is automatic  < $6,000 for complete wifi, solar gigapixel system
  53. 53. Unmanned Aerial Systems (UAV/UAS) • Tech is very new – Getting much easier & cheaper VERY quickly • Current regs are restrictive • But anyone can get started now for <$1,000 • Typically weekly or monthly repeat flights
  54. 54. Unmanned Aerial Systems (UAV/UAS) • Tech is very new – Getting much easier & cheaper VERY quickly • Current regs are restrictive • But anyone can get started now for <$1,000 • Typically weekly or monthly repeat flights Gatewing (Trimble), ~$90,000 Sensefly.com, ~$15-30K Custom built, Chris Gough CanberraUAV (2KG payload) Pocket Drone: $450 20min flight time GoPro Mount Control with tablet Phantom 2 $700 on eBay GoPro gimbal ptz Control w/ phone
  55. 55. 3D Reconstruction from UAV images • 5cm resolution 3D point cloud from UAV images (DEM/orthorectified, etc). – Software Cost: <$10K or $400/mo. Rental: pix4d.com • UAV-ready 360 degree video (hardware + software): < $6,000 AUD (kolor.com/video) http://www.sphericalimages.com/
  56. 56. http://www.youtube.com/watch?v=-11Sb531lPs Building a 6mm resolution 3D mesh from UAV images
  57. 57. Sequencing and microclimate sensors Sequencing: • Reduced representation plant genome sequence costs < $50/ plant – Should be $10/plant within a few years, then ever cheaper
  58. 58. Sequencing and microclimate sensors Sequencing: • Reduced representation plant genome sequence costs < $50/ plant – Should be $10/plant within a few years, then ever cheaper Microclimate Sensors • Currently expensive: ~$700/node. Will be <$100/node soon
  59. 59. Sequencing and microclimate sensors Sequencing: • Reduced representation plant genome sequence costs < $50/ plant – Should be $10/plant within a few years, then ever cheaper Microclimate Sensors • Currently expensive: ~$700/node. Will be <$100/node soon National Arboretum Phenomic Sensor Array (Funded!) • 30 wireless mesh sensors measure microclimate – Above ground: Temp/HG/Par – Below Ground: Soil Temp / Moisture • Micro-resolution wifi dendrometers – 20 trees • Two gigavision cameras • All data live online in realtime • Sequence all trees in study site • Track phenology and survivorship along w/ microclimate • UAV overflights (probably monthly) via CanberraUAV
  60. 60. Developing an International Phenocam Network Everyone is installing cameras now because they are cheap Cheap IP cameras on eBay
  61. 61. Developing an International Phenocam Network Everyone is installing cameras now because they are cheap The challenge: • Get everyone on board using the same cameras and protocols Cheap IP cameras on eBay
  62. 62. Developing an International Phenocam Network Everyone is installing cameras now because they are cheap The challenge: • Get everyone on board using the same cameras and protocols • Standardization of camera type – And rigorous testing protocols for new models Cheap IP cameras on eBay
  63. 63. Developing an International Phenocam Network Everyone is installing cameras now because they are cheap The challenge: • Get everyone on board using the same cameras and protocols • Standardization of camera type – And rigorous testing protocols for new models • Build automated data extraction tools that can be widely used Cheap IP cameras on eBay
  64. 64. Developing an International Phenocam Network Everyone is installing cameras now because they are cheap The challenge: • Get everyone on board using the same cameras and protocols • Standardization of camera type – And rigorous testing protocols for new models • Build automated data extraction tools that can be widely used • What about QA/QC? Cheap IP cameras on eBay
  65. 65. TERN is uniquely suited to help facilitate an international phenocam network TERN can lead in: • Collecting long-term datasets phenocam from all of its sites – Good long term data – Ground truth
  66. 66. TERN is uniquely suited to help facilitate an international phenocam network TERN can lead in: • Collecting long-term datasets phenocam from all of its sites – Good long term data – Ground truth • Providing support and authority to the development of standardized protocols
  67. 67. TERN is uniquely suited to help facilitate an international phenocam network TERN can lead in: • Collecting long-term datasets phenocam from all of its sites – Good long term data – Ground truth • Providing support and authority to the development of standardized protocols • Building and promoting collaboration with other national and international phenocam efforts – NEON phenocam workshop (October 2013) – ACEAS phenocam workshop (March 2014) – Asia, Europe?
  68. 68. TERN is uniquely suited to help facilitate an international phenocam network TERN can lead in: • Collecting long-term datasets phenocam from all of its sites – Good long term data – Ground truth • Providing support and authority to the development of standardized protocols • Building and promoting collaboration with other national and international phenocam efforts – NEON phenocam workshop (October 2013) – ACEAS phenocam workshop (March 2014) – Asia, Europe? • Developing methods for handling big data and data interoperability
  69. 69. Enabling Phenocam networks: How do we get everyone on board? • Reduce barriers to participation at all levels – Google method… • Make using their tools cheaper and easier than anyone other • Provide significant value-added for users at low or no cost
  70. 70. Enabling Phenocam networks: How do we get everyone on board? • Reduce barriers to participation at all levels – Google method… • Make using their tools cheaper and easier than anyone other • Provide significant value-added for users at low or no cost • Provide turn-key hardware systems – Lots of cameras available, but not all cameras are created equally – Work with vendors to create turnkey hardware options? – Pre-configured – Robust – Easy to install, use and maintain
  71. 71. Enabling Phenocam networks: How do we get everyone on board? • Reduce barriers to participation at all levels – Google method… • Make using their tools cheaper and easier than anyone other • Provide significant value-added for users at low or no cost • Provide turn-key hardware systems – Lots of cameras available, but not all cameras are created equally – Work with vendors to create turnkey hardware options? – Pre-configured – Robust – Easy to install, use and maintain • Provide free tools for – Free or low cost data storage – Consensus data products with QC/QA – Desktop and web playback and analysis tools that are free or low cost if data complies with standards
  72. 72. Enabling Phenocam networks: How do we get everyone on board? • Reduce barriers to participation at all levels – Google method… • Make using their tools cheaper and easier than anyone other • Provide significant value-added for users at low or no cost • Provide turn-key hardware systems – Lots of cameras available, but not all cameras are created equally – Work with vendors to create turnkey hardware options? – Pre-configured – Robust – Easy to install, use and maintain • Provide free tools for – Free or low cost data storage – Consensus data products with QC/QA – Desktop and web playback and analysis tools that are free or low cost if data complies with standards • Data can be hosted anywhere as long as it is standardized and discoverable
  73. 73. Let’s build a phenocam network where it takes 1 minute to sign up
  74. 74. Let’s build a phenocam network where it takes 1 minute to sign up
  75. 75. Let’s build a phenocam network where it takes 1 minute to sign up
  76. 76. Let’s build a phenocam network where it takes 1 minute to sign up • Archives are automatically and stored in permanent archive solution • User gets instant embed codes for putting the timelapse and data on their site • Timelapse and data can be embedded anywhere on any other sites • Users can create bookmarks of datasets to send to others
  77. 77. Let’s build a phenocam network where it takes 1 minute to sign up • Archives are automatically and stored in permanent archive solution • User gets instant embed codes for putting the timelapse and data on their site • Timelapse and data can be embedded anywhere on any other sites • Users can create bookmarks of datasets to send to others Funded ! (NCRIS phenomics infrastructure)
  78. 78. http://www.uvu.edu/crfs/livefeed/http://phenocam.sr.unh.edu/webcam/sites/bartlettir/ Data/Image visualization http://www.doublejackauctions.com/pheno/2012/ Visualization needs to: • Enhance research usability • Improve collaboration • Enhance education and outreach opportunities
  79. 79. Final questions • I always focus on things from a “capacity” perspective because I think more data is always better so When we are no longer limited by data or interfaces what science would we do?
  80. 80. Final questions • I always focus on things from a “capacity” perspective because I think more data is always better so When we are no longer limited by data or interfaces what science would we do? • All the pieces exists to build these systems how do we get from here to there? What can we do first?
  81. 81. Final questions • I always focus on things from a “capacity” perspective because I think more data is always better so When we are no longer limited by data or interfaces what science would we do? • All the pieces exists to build these systems how do we get from here to there? What can we do first? • How can we best enable collaborations that enhance our collective ability to advance near-surface remote sensing?
  82. 82. Final questions • I always focus on things from a “capacity” perspective because I think more data is always better so When we are no longer limited by data or interfaces what science would we do? • All the pieces exists to build these systems how do we get from here to there? What can we do first? • How can we best enable collaborations that enhance our collective ability to advance near-surface remote sensing? • End users – what do you need?
  83. 83. Final questions • I always focus on things from a “capacity” perspective because I think more data is always better so When we are no longer limited by data or interfaces what science would we do? • All the pieces exists to build these systems how do we get from here to there? What can we do first? • How can we best enable collaborations that enhance our collective ability to advance near-surface remote sensing? • End users – what do you need? • What are the core science questions near-remote sensing can better answer?
  84. 84. The pace of change is accelerating Panono (panono.com) • 108MP instant panoramas • $600AUD • Indiegogo: $1.2 M USD Oculus Rift (oculusvr.com) • Immersive 3D VR goggles • $350AUD • Kickstarter: $2.4 Million USD Structure 3d scanner (structure.io/) • 2mm res 3D scanner for ipads • Fully hackable with open SDK • $350AUD • Kickstarter: $1.3M USD Some new crowd funded tech from just last year Kickstarter has raised $1 billion USD in donations since 2009
  85. 85. media.pixelcase.com/360video/huntervalley/index.html
  86. 86. How do we process all this stuff?! • In < 5 years Google has created 360 deg panoramas of 5 million miles of streets (20 petabytes of geo referenced data) 1 Images • Facebook – 350 million (mostly georeferenced) images uploaded / day • A picture a minute, 15hrs a day from 60 NEON sites for 18 years is < 350 million – 250 billion images stored (with backup and instant retrieval) (1) http://www.engadget.com/2012/06/06/google-street-view-20-petabytes/ (2) http://www.google.com/maps/about/behind-the-scenes/streetview/
  87. 87. Credits & Thanks Justin Borevitz and the Borevitz Lab, ANU borevitzlab.anu.edu.au Gigavision Camera Project Justin Borevitz, U. Chicago, Now ANU Christopher Zimmermann, (Time-Science.com) Phenocam Projects Utah & Nevada Phenocams: - Pamela Nagler, USGS; Kevin Hultine, DBG FNQ phenocam: Mike Liddell, TERN / Supersite Network US Phenocam Network (Hardware and protocols): - Andrew Richardson, Harvard Funding - ACEAS: Phenocam workshop - FNQ Camera (who funded the FNQ camera?) - NEON/NSF: US Phenocam Workshop - NCRIS: Phenocam camera admin server - ANU Major Equipment Grant: National Arboretum sensor array Find me here: bit.ly/Tim_ANU WEB: borevitzlab.anu.edu.au Find me here: http://bit.ly/Tim_ANU Or Google: Tim Brown anu

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