Columbia Basin Fish and Wildlife Program Columbia Basin Fish and Wildlife Program
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Project Summary

Project 2018-002-00 - Integrated In-stream PIT tag Detection System Operations and Maintenance
Project Number:
Integrated In-stream PIT tag Detection System Operations and Maintenance
In-stream PIT tag Detection Systems (IPTDS) are installed, operated, and maintained under numerous Bonneville Power Administration (BPA) contracts. For example, direct contract and/or subcontract actions across

Project 2018-002-00 was created to provide operations and maintenance (O&M) for Instream PIT tag Detection Systems (IPTDS) formerly funded under the Integrated Status and Effectiveness Monitoring Project (ISEMP; BPA Project Number 2003-017-00). A total of 67 ISEMP IPTDS were identified as of August 1, 2017, when project 2018-002-00 was created. It is likely that a few more ISEMP IPTDS not tracked on project inventories will be located.

This project integrates the O&M of ISEMP IPTDS under a single coordinated project. This strategy is similar to the O&M strategy currently employed for PIT tag detection at mainstem hydropower facilities.

Expected near-term objectives of this project include:
1. Improvements in site reliability via implementation of infrastructure standards and routine O&M by subject matter experts.
2. Improvements in data quality resulting from infrastructure standards, routine O&M, and data management.
3. Reduced year-to-year variation in O&M costs.
4. Improved IPTDS repair and intelligent upgrade strategies.
5. Cost-savings achieved via reduced O&M labor expenses and contract pricing for IPTDS components and modem airtime plans.

Expected long-term objectives of this project include:
1. Comprehensive guidance documents; including:
a) Standard O&M practices and procedures.
b) Troubleshooting procedures.
c) IPTDS site-selection and infrastructure selection.
d)Radio-Frequency Identification (RFID) training.
e) Remote communications and data management.
2. Better coordination with RFID equipment manufacturers to guide the development of innovations.
3. Improved accountability.

Implementation of this program will proceed as follows:
1. A site audit will be completed in fall 2017 for each of the 67 existing IPTDS. This site audit will form the basis of a formal report to BPA describing:
a) equipment inventory by site;
b) status of infrastructure
c) permit status;
d) site access maps/directions;
e) an assessment of site longevity, risk, and reliability; and
f) a site-by-site proposal to improve data quality.
2. Implementation of site decommissioning, repair, or reinstallation will occur in spring 2018.
3. The standard O&M rotation will begin in fall 2018, and continue at the discretion of BPA.
This contract includes the following components:
1. A primary contract awarded to Quantitative Consultants, Inc. to serve as the primary technical O&M entity, develop reports, manage inventory, manage power and communications services, manage data, and order equipment.
2. Two subcontracts to fund a geographically distributed network of trained “first-responders.”
Proponent Orgs:
Quantitative Consultants Inc (Private)
Starting FY:
Ending FY:
Implementation - Project Status Report
Province Subbasin %
Basinwide - 100.00%
Artificial Production
RM and E
Focal Species:
Chinook - Mid-Columbia River Spring ESU
Chinook - Snake River Spring/Summer
Chinook - Snake River Spring/Summer ESU
Chinook - Upper Columbia River Spring ESU
Chinook - Upper Columbia River Summer/Fall ESU
Sockeye - Snake River ESU
Steelhead - Middle Columbia River DPS
Steelhead - Snake River DPS
Steelhead - Upper Columbia River DPS
Species Benefit:
Anadromous: 100.0%   Resident: 0.0%   Wildlife: 0.0%
BiOp Association:
FCRPS 2008 – view list of FCRPS 2008 BiOp Actions


No photos have been uploaded yet for this Project.

Summary of Budgets

To view all expenditures for all fiscal years, click "Project Exp. by FY"

To see more detailed project budget information, please visit the "Project Budget" page

Decided Budget Transfers  (FY2023 - FY2025)

Acct FY Acct Type Amount Fund Budget Decision Date
FY2023 Expense $935,693 From: BiOp FCRPS 2008 (non-Accord) FY23 SOY Budget Upload 06/01/2022
FY2023 Expense $387,892 From: BiOp FCRPS 2008 (non-Accord) Project start date extensions 06/09/2023
FY2024 Expense $976,863 From: BiOp FCRPS 2008 (non-Accord) FY24 SOY Budget Upload 06/01/2023

Pending Budget Decision?  No

Actual Project Cost Share

Current Fiscal Year — 2024
Cost Share Partner Total Proposed Contribution Total Confirmed Contribution
There are no project cost share contributions to show.
Previous Fiscal Years
Fiscal Year Total Contributions % of Budget
There are no cost share summaries to display from previous years.


The table below contains contracts with the following statuses: Active, Closed, Complete, History, Issued.
* "Total Contracted Amount" column includes contracted amount from both capital and expense components of the contract.
Expense Contracts:
Number Contractor Name Title Status Total Contracted Amount Dates
77087 SOW Biomark, LLC. 2018-002-00 INTEGRATED IN-STREAM PIT TAG DETECTION O&M Closed $924,428 10/1/2017 - 9/30/2018
80535 SOW Biomark, LLC. 2018-002-00 EXP INTEGRATED IN-STREAM PIT TAG DETECTION O&M Closed $944,196 10/1/2018 - 9/30/2019
83489 SOW Biomark, LLC. 2018-002-00 EXP INTEGRATED IN-STREAM PIT TAG DETECTION O&M Closed $1,006,765 10/1/2019 - 9/30/2020
86187 SOW Biomark, LLC. 2018-002-00 EXP INTEGRATED IN-STREAM PIT TAG DETECTION O&M Closed $971,241 10/1/2020 - 9/30/2021
88961 SOW Biomark, LLC. 2018-002-00 EXP INTEGRATED IN-STREAM PIT TAG DETECTION O&M Closed $920,201 10/1/2021 - 9/30/2022
91165 SOW Biomark, LLC. 2018-002-00 EXP IN-STREAM PIT TAG DETECTION O&M Issued $1,323,585 10/10/2022 - 2/29/2024

Annual Progress Reports
Expected (since FY2004):5
On time:3
Status Reports
On time:8
Avg Days Late:13

                Count of Contract Deliverables
Earliest Contract Subsequent Contracts Title Contractor Earliest Start Latest End Latest Status Accepted Reports Complete Green Yellow Red Total % Green and Complete Canceled
77087 80535, 83489, 86187, 88961, 91165 2018-002-00 EXP IN-STREAM PIT TAG DETECTION O&M Biomark, LLC. 10/01/2017 02/29/2024 Issued 24 46 9 0 6 61 90.16% 0
Project Totals 24 46 9 0 6 61 90.16% 0

The table content is updated frequently and thus contains more recent information than what was in the original proposal reviewed by ISRP and Council.

Review: 2019-2021 Mainstem/Program Support

Council Recommendation

Assessment Number: 2018-002-00-NPCC-20210310
Project: 2018-002-00 - Integrated In-stream PIT tag Detection System Operations and Maintenance
Review: 2019-2021 Mainstem/Program Support
Proposal: NPCC19-2018-002-00
Proposal State: Pending Council Recommendation
Approved Date: 8/25/2019
Recommendation: Implement
Comments: Continue implementation through next review cycle. Sponsors will describe in their next annual report how they are improving coordination among their projects, and communication with managers utilizing PIT-Tag arrays and related technology.
Part 3, Project-Specific Recommendation: Sponsors will describe in their next annual report how they are improving coordination among their projects and improving communication with managers utilizing PIT-Tag arrays and related technology.

[Background: See https:/]

Independent Scientific Review Panel Assessment

Assessment Number: 2018-002-00-ISRP-20190404
Project: 2018-002-00 - Integrated In-stream PIT tag Detection System Operations and Maintenance
Review: 2019-2021 Mainstem/Program Support
Proposal Number: NPCC19-2018-002-00
Completed Date: 5/30/2019
Final Round ISRP Date: 5/30/2019
Final Round ISRP Rating: Meets Scientific Review Criteria
Final Round ISRP Comment:

[The review of this project was postponed until the response loop deadline of April 30, for inclusion in the ISRP's final report dated May 30, 2019.]

The Integrated In-stream PIT tag Detection System (IPTDS) was designed as part of the Integrated Status and Effectiveness Monitoring Project (ISEMP) to estimate adult escapements and juvenile survival of Chinook and steelhead in high priority tributaries. This proposal describes encouraging results from two years of effort to develop and apply best management practices for the operation and maintenance of IPTDS. The proponents demonstrate that they have achieved considerable improvements in data reliability and cost savings. They also provide improved escapement estimates for Chinook and steelhead passing Lower Granite Dam as well as to tributaries of the Snake and upper Columbia rivers.

1. Objectives, Significance to Regional Programs, and Technical Background

This O&M project was developed to assume responsibility for a subset of the ISEMP-related IPTDS that has continuing utility for managers. The proponents clearly describe the importance of IPTDS to regional programs, including the Council's Fish and Wildlife Program and Research Plan, the Upper Columbia River Recovery Plan for steelhead and spring Chinook salmon, the Anadromous Salmonid Monitoring Strategy, and other regional programs. The primary goal of this project is to maintain the current set of PIT-tag arrays and to improve cost-effectiveness by automating many common labor-intensive tasks. A secondary goal is to develop operational standards to improve reliability and data quality. These goals offer hope that instream arrays can become more cost effective and might be installed more widely in the Basin to evaluate the cumulative impacts of restoration projects.

The two objectives listed in the proposal are not stated quantitatively. However, objective 1 (improve the reliability and consistency of data) is implicitly quantitative and will continue annually. Quantitative metrics have also been developed to evaluate performance in 2019. Objective 2 (data management) is vague in the proposal but somewhat clearer in the annual reports and manuals. To help evaluate project success, we encourage the proponents to develop quantitative objectives more explicitly in future proposals and reports.

The proposal states that responsibility for generating escapement estimates (as provided in the annual report for 2018) is now beyond the scope of this O&M project and will be transferred to another project in 2020. However, it is not clear if the proponents who will assume this responsibility will have the necessary expertise to maintain the code for these models and to continue to generalize their applicability to other sites. The ISRP notes that this project currently supports a valuable “repository” of highly qualified personnel with the experience to efficiently direct any future expansion of IPTDS and the models for estimating escapements.

2. Results and Adaptive Management

The proponents have improved the cost-effectiveness of the project and the reliability and consistency of IPTDS data by implementing remote communications at all project sites. Consolidating IPTDS within one project has substantially reduced the cost of remote communications and enabled near-real-time alerts when IPTDS diagnostics deviate from operational tolerances. Periods of inoperability have also been reduced with a corresponding improvement in data quality.

Sophisticated models developed by ISEMP were used to estimate adult escapements for 23 populations of Snake River Basin spring/summer Chinook salmon and 15 populations of steelhead.

Neither the proposal nor the annual reports describe an adaptive management process by which adjustments to infrastructure are being made. The proposal states “Development, implementation and routine updates to IPTDS site and infrastructure selection and O&M best management practices documents are the primary forms of internal adaptive management.” The proponents describe changes in methods to improve the reliability of counts while also reducing overall costs. For example, program improvements have reduced labor to repair corrupted data from 680 to 60 hours per year and reduced remote data transmission costs by 85%. The proponents also note that this project has triggered a number of cost-saving adaptive responses within the Nez Perce management process by confirming the effectiveness of IPTDS at several sites and by detecting unexpectedly high steelhead escapements at Big Sheep Creek. However, it is not clear how the project proponents receive and act on feedback from other investigators analyzing IPTDS data. How, for example, would the CSS team inform the proponents of any changes needed in the location of the project’s arrays or the need to add additional ones, e.g., at a critical junction of two streams?

In summary, this project provides new knowledge on methods for monitoring status and trends, and this knowledge is broadly applicable throughout the Columbia Basin. The project provides data needed for harvest management and evaluations of status of ESA-listed populations, as well as to assess the cumulative effectiveness of restoration efforts. Electronic data are shared directly with PTAGIS. Annual reporting is timely and includes appropriate detail.

3. Methods: Project Relationships, Work Types, and Deliverables

The proposal and annual reports include appropriate detail about the operation and maintenance of IPTDS. Project deliverables are described in detail, including (1) install fish monitoring equipment, (2) transfer and store IPTDS data, (3) IPTDS O&M Schedule, Checklist, and Troubleshooting Guide, (4) BiOp reports, (5) produce 2017/2018 steelhead escapement estimates, and (6) produce 2018 spring/summer Chinook salmon escapement estimates.

Sophisticated models are used to estimate escapements past Lower Granite Dam and into upper tributaries. The modeling approach was previously developed and used as part of ISEMP and appears reasonable. The models include: (1) an automated system (PITCleanR) is used to query interrogation data and identify the most likely final spawning destination for PIT-tagged individuals that adopt linear and non-linear migrations; (2) the State-Space Dam Escapement Model (STADEM) generates a single estimate of natural-origin escapement past Lower Granite Dam by combining data from window counts, historical estimates of nighttime passage, adult trap interceptions, and PIT tag interrogation; and (3) the Dam Branch Occupancy Model (DABOM) which expands upstream PIT tag interrogations to estimate escapement. The proposal includes links to reports that explain each of these methods in appropriate detail.


The proponents assessed the adequacy of adult abundance estimates from IPTDS data by comparing them to estimates from other methods (i.e., weirs and redd counts). The results are encouraging and have provided confidence to use IPTDS for long-term status and trend monitoring in locations not amenable to other methods and to replace more costly methods in at least two locations. However, the ISRP is concerned that DABOM is used to generate escapement estimates at very fine spatial scales such that escapement estimates to some tributaries are <50 fish (Tables 6 to 8 in the annual report). We wonder if these fine-scale estimates are precise enough to be useful. Precision improves as estimates are aggregated at larger scales (Table 9). At what scale have the modeling results been validated by fence counts? More formal review by a peer-reviewed journal and/or by the ISAB/ISRP seems warranted.

Documentation Links:

Project Relationships: None

Name Role Organization
Christopher Beasley (Inactive) Interested Party Quantitative Consultants Inc
Martin Allen Project Manager Bonneville Power Administration
Tim Copeland Interested Party Idaho Department of Fish and Game (IDFG)
William Schrader Interested Party Idaho Department of Fish and Game (IDFG)
Jay Deason Interested Party Washington Department of Fish and Wildlife (WDFW)
Russell Scranton Project SME Bonneville Power Administration
Kyle Meier Administrative Contact Biomark, LLC.
Ben Winkler Project Lead Biomark, LLC.
Daniel Gambetta Env. Compliance Lead Bonneville Power Administration