Amendment Three 8-31-2012:

This amendment is to 1) reduce the value of the contract to lime with FY 2012 expenses to no more then $100,000 and 2) end the contract on 9-30-2012.  The amendment reflect BPA's decision, in cooperation with the USFS and the ISEMP project team that  under the recent financial conditions BPA is facing in FY 2012, the continued development of LiDAR and its use in the Upper Salmon subbasin is not a priority and as a result, this amendment is required. (DByrnes).

Amendment Two:
This second amendment is a no-cost time extension due to the aircraft damage that occurred during the required annual inspection during summer 2011, and this aircraft is required to fly the LiDAR equipment package.  While towing the plane, the aircraft maintenance facility broke the ground steering mechanism making it impossible to taxi, takeoff & land.  Because of delays in deliveries of the replacement parts coming from Switzerland, the plane has yet to be repaired.  The data acquisition was originally planned for September/October, however once the aircraft is fixed, the USGS requires 6-8 weeks to complete the new LiDAR installation, conduct local test flights, and resolve any issues that crop up before any mission to acquire data.   This delay will likely push the flight period into poor weather conditions and poor instream conditions which will not allow the efficient collection of bathymetric data.  Data acquisition will occur as soon as the plane has been fixed, the LiDAR instrumentation was been tested on the flight platform and Lemhi atmospheric and instream conditions are optimal for data collection, most likely summer 2012.

Amendment One:
This no-cost time extension is to allow for the delivery and testing of the equipment, that has been delayed due to laser construction and delays in manufacturing.

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. From work completed from the previous contract,  the USGS will complete the sensor development to actually generate data of sufficient quality (point density = spatial resolution) to support useful data reduction and monitoring indicator delivery to use this instrument package for our LiDAR data acquisition this summer/fall.

This contract covers four 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, 3) LiDAR data acquisition in the Lemhi River, and 4) project oversight and administration.    The contract completion report will be submitted to NOAA fisheries for in the basin-wide ISEMP 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 (Effective 12/1/10the  support will come from a new BPA contract with Quantitative Consultants under CR 120964.]