Linking Coral Reef Remote Sensing and Field Ecology: It’s a Matter of Scale

Announcing recent publication in the Journal of Marine Science and Engineering (JMSE). The full text is available open-access online: Lucas and Goodman, JMSE, 2015, vol. 3(1): 1-20.

Authors: Matthew Q. Lucas and James Goodman

Abstract: Remote sensing shows potential for assessing biodiversity of coral reefs. Important steps in achieving this objective are better understanding the spectral variability of various reef components and correlating these spectral characteristics with field-based ecological assessments. Here we analyze >9400 coral reef field spectra from southwestern Puerto Rico to evaluate how spectral variability and, more specifically, spectral similarity between species influences estimates of biodiversity. Traditional field methods for estimating reef biodiversity using photoquadrats are also included to add ecological context to the spectral analysis. Results show that while many species can be distinguished using in situ field spectra, the addition of the overlying water column significantly reduces the ability to differentiate species, and even groups of species. This indicates that the ability to evaluate biodiversity with remote sensing decreases with increasing water depth. Due to the inherent spectral similarity amongst many species, including taxonomically dissimilar species, remote sensing underestimates biodiversity and represents the lower limit of actual species diversity. The overall implication is that coral reef ecologists using remote sensing need to consider the spatial and spectral context of the imagery, and remote sensing scientists analyzing biodiversity need to define confidence limits as a function of both water depth and the scale of information derived, e.g., species, groups of species, or community level.

Keywords: coral reefs; remote sensing; field spectra; scale; ecology; biodiversity; conservation coral reefs; remote sensing; field spectra; scale; ecology; biodiversity; conservation

Figure 8. Estimates of biodiversity

Figure 8. Estimates of biodiversity calculated using the exponential of Shannon entropy, exp(H′), illustrating influence of increasing spectral similarity amongst reef species as a function of increasing water depth: 0* is biodiversity obtained from photoquadrats, 0** is biodiversity calculated using only those species considered prevalent or sizable enough to significantly influence the remote sensing signal (i.e., species included in the spectral measurements for this study area), and 0–10 is biodiversity calculated with consideration for optical similarities amongst species (i.e., based on hierarchical clustering of reflectance spectra as influenced by the overlying water column).


A Look at What’s New in ENVI 5.2

Earlier this month Exelis Visual Information Solutions released ENVI 5.2, the latest version of their popular geospatial analysis software.

ENVI 5.2

ENVI 5.2 includes a number of new image processing tools as well as various updates and improvements to current capabilities. We’ve already downloaded our copy and started working with the new features. Here’s a look at what’s included.

A few of the most exciting new additions to ENVI include the Spatiotemporal Analysis tools, Spectral Indices tool, Full Motion Video player, and improved integration with ArcGIS:

  • Spatiotemporal Analysis. Just like the name sounds, this feature provides users the ability to analyze stacks of imagery through space and time. Most notably, tools are now available to build a raster series, where images are ordered sequentially by time, to reproject images from multiple sensors into a common projection and grid size, and to animate and export videos of these raster series.
  • Spectral Indices. Expanding on the capabilities of the previous Vegetation Index Calculator, the new Spectral Indices tool includes 64 different indices, which in addition to analyzing vegetation can also be used to investigate geology, man-made features, burned areas and water. The tool conveniently selects only those indices that can be calculated for a given input image dependent on its spectral characteristics. So when you launch the tool you’ll only see those indices that can be calculated using your imagery.
  • Full Motion Video. ENVI 5.2 now supports video, allowing users to not just play video, but also convert video files to time-enabled raster series and extract individual video frames for analysis using standard ENVI tools. Supported file formats include Skybox SkySat video, Adobe Flash Video and Shockwave Flash, Animated GIF, Apple Quicktime, Audio Video Interleaved, Google WebM Matroska, Matroska Video, Motion JPEG and JPEG2000, MPEG-1 Part 2, MPEG-2 Transport Stream, MPEG-2 Part 2, MPEG-4 Part 12 and MPEG-4 Part 14.
  • Integration with ArcGIS. Originally introduced in ENVI 5.0, additional functionality has been added for ENVI to seamlessly interact with ArcGIS, including the ability to integrate analysis tools and image output layers in a concurrent session of ArcMap. For those working in both software domains, this helps simplify your geospatial workflows and more closely integrate your raster and vector analyses.

Other noteworthy additions in this ENVI release include:

  • New data types. ENVI 5.2 now provides support to read and display imagery from AlSat-2A, Deimos-1, Gaofen-1, Proba-V S10, Proba-V S1, SkySat-1, WorldView-3, Ziyuan-1-02C and Ziyuan-3A, as well as data formats GRIB-1, GRIB-2, Multi-page TIFF and NetCDF-4.
  • NNDiffuse Pan Sharpening. A new pan sharpening tool based on nearest neighbor diffusion has been added, which is multi-threaded for high-performance image processing.
  • Scatter Plot Tool. The previous scatter plot tool has been updated and modernized, allowing users to dynamically switch bands, calculate spectral statistics, interact with ROIs, and generate density slices of the displayed spectral data.
  • Raster Color Slice. This useful tool has also been updated, particularly from a performance perspective, providing dynamic updates in the image display according to parameter changes made in the tool.

For those interested in implementing ENVI in the cloud, the ENVI 5.2 release also marks the release of ENVI Services Engine 5.2 , which is an enterprise version of ENVI that facilitates on-demand, scalable, web-based image processing applications. As an example, HySpeed Computing is currently developing a prototype implementation of ESE for processing hyperspectral imagery from the HICO sensor on the International Space Station. The HICO Image Processing System will soon be publically available for testing and evaluation by the community. A link to access the system will be provided on our website once it is released.


To learn about the above features, and many more not listed here, see the video from Exelis VIS and/or read the latest release notes on ENVI 5.2.

We’re excited to put the new tools to work. How about you?

Celebrating a Milestone – HySpeed Computing Blog Reaches 10,000 Views

HySpeed Computing 10000We would like to thank the community and all our followers for making the HySpeed Computing blog a success.  We appreciate your support and look forward to providing you many more informative posts.

Notable highlights and achievements for the blog include:

Let us know what topics you would like to see included.

Thank you!

VISualize 2014 – Call for abstracts now open

UPDATE (6-April-2015): Announcing the ENVI Analytics Symposium – taking place in Boulder, CO from August 25-26, 2015. Those looking for the VISualize symposium, which has been indefinitely postponed, should consider attending the inaugural ENVI Analytics Symposium as a great opportunity to explore the next generation of geoanalytic solutions.

Just announced!  VISualize 2014, the annual IDL & ENVI User Group Meeting hosted by Exelis Visual Information Solutions, will be taking place October 14-16 at the World Wildlife Fund in Washington, DC.

HySpeed Computing is honored to once again be co-sponsoring this year’s VISualize. We are excited to speak with you and see your latest remote sensing applications.

At this year’s meeting HySpeed Computing will be presenting results from our latest project – a prototype cloud computing system for remote sensing image processing and data visualization. We hope to see you there.

Abstract submission deadline is September 12. Register today!


“Please join us at VISualize 2014, October 14th – 16th, at the World Wildlife Fund in Washington, DC. This three day event explores real-world applications of ENVI and IDL with a specific focus on Modern Approaches for Remote Sensing & Monitoring Environmental Extremes.

Suggested topics include:

  • Using new data platforms such as UAS, microsatellites, and SAR sensors for environmental assessments
  • Land subsidence monitoring and mapping techniques
  • Remote sensing solutions for precision agriculture mapping
  • Drought, flood, and extreme precipitation event monitoring and assessment
  • Wildfire and conservation area monitoring, management, mitigation, and planning
  • Monitoring leaks from natural gas pipelines

Don’t miss this excellent opportunity to connect with industry thought leaders, researchers, and scientists.”

Register today!


NASA Takes Over Navy Instrument On ISS

A version of this article appears in the May 19 edition of Aviation Week & Space Technology, p. 59, Frank Morring, Jr.

HREP on JEMEFA hyperspectral imager on the International Space Station (ISS) that was developed by the U.S. Navy as an experiment in littoral-warfare support is finding new life as an academic tool under NASA management, and already has drawn some seed money as a pathfinder for commercial Earth observation.

Facing Earth in open space on the Japanese Experiment Module’s porchlike Exposed Facility, the Hyperspectral Imager for Coastal Oceans (HICO) continues to return at least one image a day of near-shore waters with unprecedented spectral and spatial resolution.

HICO was built to provide a low-cost means to study the utility of hyperspectral imaging from orbit in meeting the Navy’s operational needs close to shore. Growing out of its experiences in the Persian Gulf and other shallow-water operations, the Office of Naval Research wanted to evaluate the utility of space-based hyperspectral imagery to characterize littoral waters and conduct bathymetry to track changes over time that could impact operations.

The Naval Research Laboratory (NRL) developed HICO, which was based on airborne hyperspectral imagery technology and off-the-shelf hardware to hold down costs. HICO was launched Sept. 10, 2009, on a Japanese H-2 transfer vehicle as part of the HICO and RAIDS (Remote Atmospheric and Ionospheric Detection System) Experimental Payloads; it returned its first image two weeks later.

In three years of Navy-funded operations, HICO “exceeded all its goals,” says Mary Kappus, coastal and ocean remote sensing branch head at NRL.

“In the past it was blue ocean stuff, and things have moved more toward interest in the coastal ocean,” she says. “It is a much more difficult environment. In the open ocean, multi-spectral was at least adequate.”

NASA, the U.S. partner on the ISS, took over HICO in January 2013 after Navy funding expired. The Navy also released almost all of the HICO data collected during its three years running the instrument. It has been posted for open access on the HICO website managed by Oregon State University.

While the Navy program was open to most researchers, the principal-investigator approach and the service’s multistep approval process made it laborious to gain access on the HICO instrument.

“[NASA] wanted it opened up, and we had to get permission from the Navy to put the historical data on there,” says Kappus. “So anything we collect now goes on there, and then we ask the Navy for permission to put old data on there. They reviewed [this] and approved releasing most of it.”

Under the new regime NRL still operates the HICO sensor, but through the NASA ISS payload office at Marshall Space Flight Center. This more-direct approach has given users access to more data and, depending on the target’s position relative to the station orbit, a chance to collect two images per day instead of one. Kappus explains that the data buffer on HICO is relatively small, so coordination with the downlink via the Payload Operations Center at Marshall is essential to collecting data before the buffer fills up.

Task orders are worked through the same channels. Presenting an update to HICO users in Silver Spring, Md., on May 7, Kappus said 171 of 332 total “scenes” targeted between Nov. 11, 2013, and March 12 were requested by researchers backed by the NRL and NASA; international researchers comprised the balance.

Data from HICO is posted on NASA’s Ocean Color website, where usage also is tracked. After the U.S., “China is the biggest user” of the website data, Kappus says, followed by Germany, Japan and Russia. The types of data sought, such as seasonal bathymetry that shows changes in the bottom of shallow waters, has remained the same through the transition from Navy to NASA.

“The same kinds of things are relevant for everybody; what is changing in the water,” she says.

HICO offers unprecedented detail from its perch on the ISS, providing 90-meter (295-ft.) resolution across wavelengths of 380-960 nanometers sampled at 5.7 nanometers. Sorting that rich dataset requires sophisticated software, typically custom-made and out of the reach of many users.

To expand the user set for HICO and future Earth-observing sensors on the space station, the Center for the Advancement of Science in Space, the non-profit set up by NASA to promote the commercial use of U.S. National Laboratory facilities on the ISS, awarded a $150,000 grant to HySpeed Computing, a Miami-based startup, and [Exelis] to demonstrate an online imaging processing system that can rapidly integrate new algorithms.

James Goodman, president/CEO of HySpeed, says the idea is to build a commercial way for users to process HICO data for their own needs at the same place online that they get it.

“Ideally a copy of this will [be] on the Oregon State server where the data resides,” Goodman says. “As a HICO user you would come in and say ‘I want to use this data, and I want to run this process.’ So you don’t need your own customized remote-sensing software. It expands it well beyond the research crowd that has invested in high-end remote-sensing software. It can be any-level user who has a web browser.”

HySpeed Computing Announces New Project – Remote Sensing on the International Space Station

CASIS Reaches Agreement with HySpeed Computing and Exelis for Hyperspectral Image Analysis Using Cloud Computing

Originally published by CASIS on February 20, 2014


KENNEDY SPACE CENTER, FL. (February 20th, 2014) – The Center for the Advancement of Science in Space (CASIS) today announced an agreement with HySpeed Computing and Exelis for a project demonstrating cloud computing capabilities for image processing and remote sensing applications on the International Space Station (ISS). CASIS was selected by NASA in July 2011 to maximize use of the ISS U.S. National Laboratory.

HySpeed Computing and Exelis plan to develop a prototype online, on-demand image processing system using example data from the Hyperspectral Imager for the Coastal Ocean (HICO). The system will leverage the recently released ENVI Services Engine, and include a web-interface for users to access a collection of image processing applications derived from the HICO user community.

HICO is a hyperspectral instrument specializing in visible and near-infrared camera technology, designed specifically for imaging the coastal zone and ocean waters. HICO is part of the first U.S. experiment payload on the Japanese Experiment Module – Exposed Facility (JEM-EF) on the International Space Station (ISS), and has acquired thousands of images from around the globe since its launch in 2009.

“We are excited to be supported by CASIS,” said HySpeed Computing President James Goodman. “We believe this project will demonstrate an effective pathway for inspiring innovation and facilitating technology transfer in the geospatial marketplace.”

“This partnership with HySpeed Computing and Exelis is another example of leveraging existing assets onboard the ISS for terrestrial benefit,” said CASIS Director of Operations, Ken Shields. “During its existence, HICO has proven to be a dynamic camera capable of delivering the unique vantage point of the ISS to better understand our oceans and shorelines.”

For information about CASIS opportunities, including instructions on submitting research ideas, please visit:

Additionally, CASIS currently has a solicitation in remote sensing open to the research community. Letters of intent are required to move forward in the proposal process. Letters of intent are due tomorrow, February 21, 2014. To learn more visit:

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About CASIS: The Center for the Advancement of Science in Space (CASIS) was selected by NASA in July 2011 to maximize use of the International Space Station (ISS) U.S. National Laboratory through 2020. CASIS is dedicated to supporting and accelerating innovations and new discoveries that will enhance the health and wellbeing of people and our planet. For more information, visit:

About the ISS National Laboratory: In 2005, Congress designated the U.S. portion of the International Space Station as the nation’s newest national laboratory to maximize its use for improving life on Earth, promoting collaboration among diverse users and advancing STEM education. This unique laboratory environment is available for use by other U.S. government agencies and by academic and private institutions, providing access to the permanent microgravity setting, vantage point in low earth orbit and varied environments of space.

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Source: Feb 20, 2014 CASIS press release.

HySpeed Computing Blog Reaches 5000 Views – And other milestones

HySpeed Computing Milestones

HySpeed Computing is celebrating a milestone of reaching over 5000 views for our blog.

We would like to thank the community and all our followers for making the blog a success. We’re looking forward to expanding this initiative and continuing to deliver you informative content.

Notable highlights for the blog from the past year include:

Additional accomplishments from our other information resources include:

  • The HySpeed Computing website has now garnered over 3000 pageviews.
  • Our LinkedIn page has achieved over 7500 impressions.
  • The total reach of our Facebook page has greater than 8000 views with more than 38,000 impressions.
  • You can also now find HySpeed Computing on our Google+ page.

We appreciate your support and encourage you to invite others to join in our discussion. Thank you!

HyPhoon – Announcing Launch of Geospatial Data Sharing Service

HySpeed computing is proud to announce the release of HyPhoon, a community gateway for the access and exchange of datasets, applications and knowledge.

The inaugural dataset offered through HyPhoon is from Heron Reef, Australia, provided courtesy of the Center for Spatial Environmental Research at the University of Queensland.

Heron ReefHeron Reef (32 km^2) is located at the southern end of the Great Barrier Reef and has been a focus of coral reef research since the early 1900s. The reef contains Heron Island, which hosts one of the longest running, most significant, coral reef research stations in the world. One of the first large scale reef mapping projects in the world was developed on Heron Reef in the 1980s. Since the late 1990s the Biophysical Remote Sensing Group at the University of Queensland has developed and tested remote sensing applications on Heron Reef with collaborators from around Australia and the rest of the world.

Data offered for the Heron Reef dataset currently includes:

  • mosaic of 2002 CASI hyperspectral imagery at 1 m spatial resolution
  • field transects from 2002 of substrate cover for 3,586 photos
  • depth measurements from 2007 for 7,462 individual soundings
  • bathymetric map derived from the 2002 CASI imagery
  • habitat map derived from 2007 QuickBird imagery
  • geomorphic zonation derived from 2007 QuickBird imagery

This data is offered using the Creative Commons Attribution license (CC BY 3.0 Unported), which “lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation.”

The data from HyPhoon is available for the community to use in research projects, class assignments, algorithm development, application testing and validation, and in some cases also commercial applications. In other words, in the spirit of encouraging innovation, these datasets are offered as a community resource and open to your creativity.

We welcome your thoughts for new data you would like to see included, and also encourage you to contribute your own data or derived products to showcase on HyPhoon.

To access HyPhoon:


A Look at What’s New in ENVI 5.1

ENVI 5.1(16-Dec-2013) Today Exelis Visual Information Solutions released ENVI 5.1, the latest version of their popular geospatial analysis software.

We’ve already downloaded and installed our copy, so read below if you want to be one of the first to learn about the new features. Or better yet, if you or your organization are current with the ENVI maintenance program, you too can download the new version and start using it yourself today.

Below are a few highlights of the new features in ENVI 5.1:

  • Region of Interest (ROI) Tool. Previously only accessible in ENVI Classic, users can now define and manage ROIs in the new interface. This includes the ability to manually draw ROIs, generate ROIs from band thresholds, grow existing ROIs, and create multi-part ROIs. Additionally, ROIs are now stored as georeferenced features, which means they can be easily ported between images.
  • Seamless Mosaic Workflow. The Georeferenced Mosaicking tool has been replaced with the new Seamless Mosaic Workflow. This tool allows user to create high quality seamless mosaics by combing multiple georeferenced scenes. Included is the ability to create and edit seamlines, perform edge feathering and color correction, and export finished mosaics to ENVI or TIFF formats.  Also included are tutorials and tutorial data to learn the simple and advanced features of this workflow.
  • Spectral Data. Both the Spectral Profile and Spectral Library viewers include improvements for visualizing and analyzing spectral data. The software also includes updated versions of four key spectral libraries: ASTER Spectral Library Version 2, U.S. Geological Survey Digital Spectral Library 06, Johns Hopkins University Spectral Library, and the NASA Jet Propulsion Laboratory Spectral Library.
  • Additional Data Types. ENVI 5.1 can now open generic HDF5 files, which includes data distributed from sensors like NPP VIIRS, SSOT, ResourceSat-2, and HICO. Additional data types and file formats also now supported include ECRG, GeoEye-1 in DigitalGlobe format, Goktuk-2, KOMPSAT-3, NigeriaSat-1 and -2, RASAT, and others.
  • Added Landsat 8 Support. Various improvements have been included for the handling of Landsat 8 data, such as automatically reading the thermal infrared coefficients from the associated metadata, including the Quality and Cirrus Cloud bands in the Data and Layer Managers, correcting reflectance gains and offsets for solar elevation, and updating FLAASH to process Landsat 8 imagery.

These and other welcome improvements continue to expand the capabilities of ENVI, and we’re excited to start working with the new features.

For more on ENVI:

EnMAP Coral Reef Simulation – The first of its kind

The GFZ German Research Center for Geosciences and HySpeed Computing announce the first ever simulation of a coral reef scene using the EnMAP End-to-End Simulation tool. This synthetic, yet realistic, scene of French Frigate Shoals will be used to help test marine and coral reef related analysis capabilities of the forthcoming EnMAP hyperspectral satellite mission.

EeteS EnMAP Simulation FFS

EeteS simulation of EnMAP scene for French Frigate Shoals, Hawaii

EnMAP (Environmental Mapping and Analysis Program) is a German hyperspectral satellite mission scheduled for launch in 2017. As part of the satellite’s development, the EnMAP End-to-End Simulation tool (EeteS) was created at GFZ to provide accurate simulation of the entire image generation, calibration and processing chain. EeteS is also being used to assist with overall system design, the optimization of fundamental instrument parameters, and the development and evaluation of data pre-processing and scientific-exploitation algorithms.

EeteS has previously been utilized to simulate various terrestrial scenes, such as agriculture and forest areas, but until now had not previously been used for generating a coral reef scene. Considering the economic and ecologic importance of coral reef ecosystems, the ability to refine existing analysis tools and develop new algorithms prior to launch is a critical step towards efficiently implementing new reef remote sensing capabilities once EnMAP is operational.

The input imagery for the French Frigate Shoals simulation was derived from a mosaic of four AVIRIS flightlines, acquired in April 2000 as part of an airborne hyperspectral survey of the Northwestern Hawaiian Islands by NASA’s Jet Propulsion Laboratory. Selection of this study area was based in part on the availability of this data, and in part due to the size of the atoll, which more than adequately fills the full 30 km width of an EnMAP swath. In addition to flightline mosaicking, image pre-processing included atmospheric and geographic corrections, generating a land/cloud mask, and minimizing the impact of sunglint. The final AVIRIS mosaic was provided as a single integrated scene of at-surface reflectance.

For the EeteS simulation, the first step was to transform this AVIRIS mosaic into raw EnMAP data using a series of forward processing steps that model atmospheric conditions and account for spatial, spectral, and radiometric differences between the two sensors. The software then simulates the full EnMAP image processing chain, including onboard calibration, atmospheric correction and orthorectification modules to ultimately produce geocoded at-surface reflectance.

The resulting scene visually appears to be an exact replica of the original AVIRIS mosaic, but more importantly now emulates the spatial and spectral characteristics of the new EnMAP sensor. The next step is for researchers to explore how different hyperspectral algorithms can be used to derive valuable environmental information from this data.

For more information on EnMAP and EeteS:

EeteS image processing and above description performed with contributions from Drs. Karl Segl and Christian Rogass (GFZ German Research Center for Geosciences).