Contract Extension:
The contract is being extended (no-cost extension) to May 31,2010 to allow for administrative processing time of procured equipment for Work Element C (LiDAR Data Extraction and Habitat Metric Development), Work Element D (Experimental Advanced Airborne Research LiDAR (EAARL) Optimization) and Work Element F (Produce Progress (Annual) Report).   The equipment was ordered by the USGS
last year, but due to time constraints involved in the administrative processing of the order and the custom build of the lasers, they will be delivered in February 2010 and assembled during the Spring of 2010.  The delays are associated with the custom built specifications of the two lasers and associated equipment that allow the instruments to fly mountain stream channels.   Once the equipment is received and assembled, the extension will cover the time necessary to ensure that the new equipment is functioning correctly and the lasers meet the order specifications.  Work will also continue with the WE C, Data extraction and Habitat metric development during this no-cost extension period with the Rocky Mountain Research Station

Amendment to Original Contract:
The overall goal of this contract was the generation of software tools to extract useful monitoring indicators from the LiDAR data sets as well as the collection of new LiDAR data that supported these monitoring indicators.  However, in order to generate the data set, the current bathymetric LiDAR sensors need further technical development.  A portion of the original contract was to support this development, and a portion was to have this sensor flown in the Lemhi River this fall.  Based on conversations with our collaborators at USFS and USGS, the sensor development will not be far enough along this fall to actually generate data of sufficient quality (point density = spatial resolution) to support useful data reduction and monitoring indicator delivery.  So, to support our long term goal of exploring, and ideally adopting this tool, we amended the USFS contract to remove the tasks associated with two Work Element's (WE B Produce Environmental Compliance Documentation, WE C LiDAR Data Acquisition - Lemhi River) that specified data collection, and reprogram these funds to WE E (Experimental Advanced Airborne Research LiDAR Optimization) for the sensor development components of the work. All other elements of the associated WE's stay the same.  The work element budget was changed to reflect the removal of WE B and C and the inclusion of those funds into WE D (which was WE E).  Work element dates also reflect the change in the type of work and the end dates correspond to the contract end date 2/28/2010.

Original Contract Summary:
Since its inception in FY2003, Project #2003-017-00 (the Integrated Status and Effectiveness Monitoring Program; ISEMP) has been developing two novel monitoring and evaluation programs: (i) subbasin-scale pilot status and trend monitoring efforts for anadromous salmonids and their habitat in the Wenatchee/Entiat, John Day and South Fork Salmon River basins, and (ii) effectiveness monitoring for suites of habitat restoration projects in selected watersheds within the three target subbasins. This work - critical for implementing the 2000 NMFS FCRPS Biological Opinion (RPA Actions 180, 181, and 183) (BiOp) and UPAs from the 2004 BiOp - builds on current status and trend monitoring programs within each of these basins. Several regional and local organizations are funding and implementing these programs. In short, this project has integrated existing and new monitoring and evaluation activities in three pilot subbasins to help ensure that provisions of the BiOp are satisfied.  

The ISEMP design proposed for the Lemhi River and South Fork Salmon River are intended to directly address key evaluation gaps that currently limit effective recovery planning and complicate the aggregation of population and habitat status and trends information to address questions at larger spatial scales.  This contract specifically addresses the habitat monitoring part of ISEMP in the Lemhi River using a new remote sensing system that combines a narrow-beam bathymetric Light Detection and Ranging (LiDAR) system and high resolution color-infrared aerial photos.  This instrument package appears to be the first of a new generation of remote sensing techniques capable of continuously measure riparian and channel characteristics in one integrated mission. These methods may allow us to monitor the physical habitat along nearly entire stream networks.
The ISEMP project is attempting to identify covariates to capacity and productivity, a product of the interactions of multiple mechanisms and response variables operating on a variety of temporal and spatial scales.  The experimental design is based on a model developed to assess changes in habitat complexity and the effect it may have on fish productivity.  Essential to the model are two components - habitat quality and quantity.  

Bathymetric or green LiDAR is currently the only technique that will map in-stream and adjacent floodplain topography with high resolution over hundreds of kilometers without local calibration and through water depths ranging from decimeters to tens of meters.  A green LiDAR also will define the three-dimensional structure of vegetation, and when combined with standard multispectral analyses of vegetation from color-infrared photos, yield a much richer description of the riparian habitat.  Because of green LiDAR’s ability to penetrate water, it offers a quantitative approach to measuring instream habitat in a continuous manner, thus vastly increasing the ability to detect changes in habitat resulting from habitat actions. Thus, this project will test a remote sensing platform that will seamlessly measure the vegetation canopy in three dimensions, the bare earth topography beneath the vegetation in the riparian zone and the morphology and physical habitat inside the channel in one data set. The system will provide an integrated view of a channel-floodplain ecosystem with a spatial resolution of about 1 meter and continuous spatial coverage of up to hundreds of kilometers of channel distance. This will allow us to evaluate habitat metrics at a wide range of spatial scales. Together with the proposed watershed model, these measurements and metrics will enable us to evaluate the impacts of habitat actions on the physical environment and on freshwater productivity.  

We will use the USGS Experimental Advanced Airborne Research LiDAR (EAARL) to continuously measure the stream channels.  EAARL has been used successfully to survey several riverine systems and streams, although never in support of models of habitat complexity and fish productivity as we propose here.  EAARL is the only available instrument (commercial or non-commercial) with the combination of water penetration and a narrow-footprint necessary to resolve small bedforms and channel banks in typical salmonid spawning and rearing streams.  The EAARL instrument package also takes high resolution color-infrared aerial photography in concert with the sub-aerial and sub-aqueous topographic measurements.  With the extent and complexity of habitat actions planned in the Salmon Sub-basin, we are interested in using LiDAR to continuously survey the Lemhi River system to estimate instream habitat quantity and other channel characteristics to parameterize the ISEMP habitat model for modeling fish population growth and survival.  In the South Fork Salmon River, the continuous coverage provided by EAARL will enable us to capture status and trends in habitat quality at a variety of spatial scales, in order to determine the scale at which such trends are most cost-effectively and reliably captured.  From previous work completed by the Rocky Mountain Research Station and United States Geological Survey, it has been shown that the data collected using EAARL is a cost-effective tool to produce precise measurements of stream channels and riparian zones, especially at the large, spatial scale of the Salmon ISEMP sub-basin when compared to traditional survey techniques. We will investigate how to use EAARL data to support the ISEMP habitat model and explore further model development that will more fully exploit the unique characteristics of the data.

Amendment to original contract: The overall goal of this contract was the generation of software tools to extract useful monitoring indicators from the LiDAR data sets as well as the collection of new LiDAR data that supported these monitoring indicators.  However, in order to generate the data set, the current bathymetric LiDAR sensors need further technical development.  A portion of the original contract was to support this development, and a portion was to have this sensor flown in the Lemhi River this fall.  Based on conversations with our collaborators at USFS and USGS, the sensor development will not be far enough along this fall to actually generate data of sufficient quality (point density = spatial resolution) to support useful data reduction and monitoring indicator delivery.  So, to support our long term goal of exploring, and ideally adopting this tool, we admended the USFS contract to remove the tasks associated with two Work Element's (WE B Produce Environmental Compliance Documentation, WE C LiDAR Data Acquisition - Lemhi River) that specified data collection, and reprogram these funds to WE E (Experimental Advanced Airborne Research LiDAR Optimization) for the sensor development components of the work.

This contract now covers three work elements necessary to evaluate the usefulness of EAARL in surveying salmonid habitat:  1) Monitoring method development through optimization of the EAARL instrument package, 2) Data extraction and habitat metric development for EAARL’s digital terrain model, and 3) project oversight and administration.    The contract completion report will be submitted to NOAA fisheries for in the basin-wide ISMEP report and to BPA according to terms of this contract.

[Note:  Jody White and Chris Beasley will serve in their respective roles (see contact list) and are fully funded under a subcontract under a related ISEMP contract (NOAA Fisheries #35962 to perform coordiantion / oversight on this contract.  Effective 12/1/08 the  support will come from a new BPA contract with Quantitative Consultants under CR 101706.]