Long Term Resource Monitoring Program

Program Report

95-P006

Geospatial Application:

Aquatic Habitat Analysis

and Visualization Tool

This PDF file may appear different from the printed report

because of slight variations incurred by electronic transmission.

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May 1995
Geospatial Application:

Aquatic Habitat Analysis and Visualization Tool

by 

Douglas A. Olsen

National Biological Service

Environmental Management Technical Center

575 Lester Avenue

Onalaska, Wisconsin 54650

May 1995
The Environmental Management Technical Center issues LTRMP Program Reports to provide

Long Term Resource Monitoring Program partners with programmatic documentation,

procedures manuals, training manuals, and geospatial applications.

National Biological Service

Environmental Management

Technical Center

CENTER DIRECTOR

Robert L. Delaney

SCIENCE ADVISOR

John W. Barko

INFORMATION AND TECHNOLOGY

SERVICES DIRECTOR

Norman W. Hildrum

GEOSPATIAL APPLICATIONS

DIRECTOR

Frank D'Erchia 

REPORT EDITOR

Terry D'Erchia

Cover graphic by Mi Ae Lipe

Mention of trade names or commercial products does not constitute endorsement or recommendation for

use by the National Biological Service, U.S. Department of the Interior.

The National Biological Service . . . gathering, analyzing,

and sharing the biological information necessary to support the wise

stewardship of the Nation's natural resources.

 Printed on recycled paper 
iii

Preface

The Long Term Resource Monitoring Program (LTRMP) was authorized under the

Water Resources Development Act of 1986 (Public Law 99-662) as an element of the U.S.

Army Corps of Engineers' Environmental Management Program. The LTRMP is being

implemented by the Environmental Management Technical Center, an office of the National

Biological Service, in cooperation with the five Upper Mississippi River System (UMRS)

states, Illinois, Iowa, Minnesota, Missouri, and Wisconsin, with guidance and Program

responsibility provided by the U.S. Army Corps of Engineers. The UMRS encompasses the

commercially navigable reaches of the Upper Mississippi River, as well as the Illinois River

and navigable portions of the Kaskaskia, Black, St. Croix, and Minnesota Rivers.

The mission of the LTRMP is to provide decision makers with information to

maintain the UMRS as a sustainable large river ecosystem given its multiple-use character.

The long-term goals of the Program are to understand the system, determine resource trends

and impacts, develop management alternatives, manage information, and develop useful

products.

The strategy to conduct spatial analysis to provide support to LTRMP Partner

activities is included in the LTRMP Operating Plan (USFWS 1992) as Strategy 1.3.2, Select

New Problems for Research, Substrategy 1, Definition and Systemic Inventory of Aquatic

Habitats, and Work Unit A, Interdisciplinary Aquatic Habitat Inventory, Mapping, and

Analysis.

This manual was developed with funding provided by the Long Term Resource

Monitoring Program.

Additional copies of this report may be obtained from the National Technical

Information Service, 5285 Port Royal Road, Springfield, Virginia 22161 (1-800-553-6847).

This report should be cited as:

Olsen, D. A. 1995. Geospatial Application: Aquatic habitat analysis and visualization tool.

National Biological Service, Environmental Management Technical Center, Onalaska,

Wisconsin. May 1995. LTRMP 95-P006. 5 pp.
v

Contents

Page

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iii

Contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v

Figures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v

Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Introduction .......................................................... 1

Aquatic Habitat Analysis and Visualization Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Finger Lakes Aquatic Habitat Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Using the Aquatic Habitat Analysis and Visualization Tool . . . . . . . . . . . . . . . . . . . . . 3

Overview of Main Menu Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

View Menu Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Figures

Page

Figure 1. Location of Finger Lakes complex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Figure 2. Habitat definition menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Geospatial Application:

Aquatic Habitat Analysis and Visualization Tool

By Douglas A. Olsen

Abstract

The Aquatic Habitat Analysis and Visualization Tool is a program and interface that allows users to view and

create habitat models using the pre-improvement water quality data collected for the Finger Lakes Habitat

Rehabilitation Project (HREP). The Finger Lakes HREP is a hydrologic modification of a backwater lake

complex in upper Pool 5 of the Mississippi River. The program and interface were implemented using Arc

Macro Language and require the workstation version of ARC/INFO geographic information system software

(ESRI, Redlands, CA).

Introduction

The Environmental Management Program

(EMP) for the Upper Mississippi River System

(UMRS) was authorized by the Water Resources

Development Act of 1986. The act authorizes the

U.S. Army Corps of Engineers (Corps), in

partnership with the U.S. Department of the

Interior and five UMRS states, to administer a

program of long-term monitoring, research, and

habitat rehabilitation on the UMRS. The National

Biological Service Environmental Management

Technical Center (EMTC) conducts long-term

monitoring of UMRS natural resources and

ecological research, and is participating in a series

of investigations associated with EMP Habitat

Rehabilitation and Enhancement Projects (HREPs).

Currently, personnel from the EMTC, the

National Fisheries Research Center, the Waterways

Experiment Station, Eau Galle Limnological

Laboratory, and the Minnesota Department of

Natural Resources are engaged in investigations in

the Finger Lakes complex. The study site consists

of six connected lakes located in UMRS Pool 5 just

downstream from the dike at Lock and Dam 4, near

Kellogg, Minnesota (Fig. 1). As noted by Barko et

al. (1993):

Several of these lakes experience low oxygen

concentrations and extreme water temperatures,

conditions that substantially reduce their

suitability for fish. To improve fish habitat, the

Corps, St. Paul District, will retrofit an existing

culvert system and install additional controlledflow culverts to regulate the hydrology of the lake

complex. Pre- and post-construction monitoring

data are being obtained by the State of Minnesota

as well as Federal participants to evaluate project

success. The Finger Lakes Project is designed to

examine the effects of management measures

directed toward fisheries improvements, with

attention also given to the effects on other

important and interrelated variables. Ongoing

studies focus on changes in hydrology, water

quality, sedimentation, vegetation, fish, and

invertebrates.

The project, authorized in FY 1991, is anticipated

to span a 4- to 5-year period.

Aquatic Habitat Analysis

and Visualization Tool

The Aquatic Habitat Analysis and Visualization

Tool was developed to provide investigators with

an adaptable geographic information system (GIS)

application to allow analysis and visualization of

the dynamic mosaic of aquatic habitat patches that

occurs in the UMRS. The tool incorporates spatial

data about aquatic habitat from the study area. The

program allows the user to interactively define

specific aquatic habitat types, analyze the spatial

and temporal occurrence of the habitat patches, and

visualize the results. The simple graphical user

interface provided can be used effectively with no

training or prior GIS knowledge. The program and

interface were implemented using Arc Macro
2

Figure 1. Location of Finger Lakes complex

Language and require the workstation version of

ARC/INFO geographic information system

software (ESRI, Redlands, CA).

Spatial data on bathymetry, substrate type,

vegetation, water temperature, and dissolved

oxygen from Lower Peterson and Third Lakes in

the Finger Lakes complex were used for

development of the pilot tool.

Finger Lakes Aquatic

Habitat Data

Bathymetric data were mapped using a shallow

draft boat equipped with a chart recorder. Survey

transects were closely spaced across the Finger

Lakes open water areas. Water surface elevation

was monitored daily at the Lock and Dam 4

tailwater.

Water temperature and dissolved oxygen data

were measured at 23 locations in Lower Peterson

Lake and at 27 locations in Third Lake. Sampling

locations were systematically located along

transects across the lakes. Data were obtained

from the same set of sampling locations

approximately biweekly during the open water

season and approximately monthly during winter

from August 1991 through August 1993. Water

temperature and dissolved oxygen were measured

near the surface (0.1 m below the surface) and near

the bottom (0.1 m above the bottom). Sampling

was conducted in the morning (approximately 0800

to 1000 h) and in the afternoon (approximately
3

1400 to 1600 h) on each sampling date. Only one

lake was sampled on each sampling date. Weather,

ice conditions, and sampling difficulties resulted in

missing data for some sampling events.

GIS techniques were used to interpolate

continuous surfaces for bathymetry, water

temperature, and dissolved oxygen from the

original point-sampled data.

Substrate type was surveyed using visual and

tactile methods at many sampling sites in Lower

Peterson and Third Lakes. GIS datasets were

manually interpolated from these sampling points.

Vegetation data were automated for 1989 and

1992 from 1:15,000-scale color-infrared aerial

photographs. Aerial photography missions were

flown during August for both years.

Using the Aquatic

Habitat Analysis and

Visualization Tool

Overview of Main

Menu Options

The ABOUT THE FINGER LAKES option

starts a slide show describing the study area, HREP

objectives, and sampling strategy.

The VIEW option brings up a menu of options

for viewing the water quality and other data.

The STATISTICS option generates statistics

about the current view. (Active only with specific

VIEW options.)

The QUIT option exits the Finger Lakes Water

Quality Visualization Tool.

View Menu Options

PETERSON LAKE brings up a menu of options

for viewing Lower Peterson Lake water

temperature or dissolved oxygen surfaces for a

single date. This option provides a side-by-side

view showing the bottom and surface data for

either the morning or afternoon sampling run. The

STATISTICS button on the main menu bar is

active when using this option.

THIRD LAKE brings up a menu of options for

viewing Third Lake water temperature or dissolved

oxygen surfaces for a single date. This option

provides a side-by-side view showing the bottom

and surface data for either the morning or

afternoon sampling run. The STATISTICS button

on the main menu bar is active when using this

option.

CUSTOM VIEW brings up a menu of options

for viewing any two available datasets side by side.

The user chooses the desired dataset for view one

(left) and pushes the "Define View One" button. If

additional data about view one is needed, a submenu will pop up. Sub-menus vary, depending

upon the dataset chosen. Bathymetry views require

the user to select a date, as the bathymetry data are

adjusted for water surface elevation on individual

sampling days. Water quality views require the

user to select a date, a sampling time (morning or

afternoon), and a sampling depth (surface or

bottom). Vegetation views require the user to

select a date (1989 or 1992). After the user applies

the sub-menu choices and pushes the "Define View

One" button, the view one definition text changes

from "Undefined" to the title of the dataset chosen.

The same procedure is followed for defining view

two. Both views must be defined prior to

execution of this menu. The STATISTICS button

on the main menu bar is not active when using this

option.

HABITAT DEFINITION brings up a menu of

options for defining a habitat for either Lower

Peterson or Third Lakes (Fig. 2). The user selects

the lake of choice and the desired sampling time

(morning or afternoon), indicating with the slider

bars in the Depth Range section the range of water

depths to use in the habitat definition. Moving the

"To" slider bar all the way to the right selects all
4

Figure 2. Habitat definition menu

depths above the "From" slider bar value. The

same procedure is used to define the ranges for

dissolved oxygen and temperature. Next, the user

selects the desired settings for "Vegetation" (absent

or present) and "Substrate" (sand or silt). Selecting

"Off" removes that habitat parameter from the

model. Clicking on the "Apply" button closes the

Habitat Definition menu and brings up the

Sampling Date menu to the right of the main

display window. The user selects a date from this

menu and clicks the "Apply" button to execute the

model for the selected date using the previously

defined habitat parameters. Areas displayed in red

are areas meeting the criteria for the defined habitat

on the selected day and sampling time. Habitat

area and volume statistics are calculated and

displayed for both sampling depths (surface and

bottom). It is assumed that the surface

measurements represent the upper half of lake

volume and the bottom measurements represent the

lower half. Volume statistics are then calculated as

1/2 depth * area. Water elevation is taken into

consideration in the calculation of habitat volumes.

Bathymetry data are corrected to the actual depth

on a given sampling day as measured at the Pool 4

tailwater. Because terrestrial floodplain elevation

data are unavailable, lake shorelines are assumed to

remain static at the elevation of 660 ft above mean

sea level.

RUN MOVIE brings up a menu of available

animations. These preselected habitat definitions

automatically cycle through all available sampling

dates, showing the spatial/temporal change in the

defined habitat.
5

Summary

The Aquatic Habitat Analysis and Visualization

Tool resulted from a preliminary investigation into

developing a GIS methodology for modeling

distribution and temporal change in aquatic

habitats. Although the first stage of the

investigation was limited to data collected from the

Finger Lakes complex in upper Pool 5, the

techniques developed are relevant to any aquatic

area where sufficient data exist. The next stage of

the investigation will focus on Lake Onalaska

(Pool 7), where more sophisticated habitat

definitions will be attained by including additional

information such as current velocity data from

numerical hydrologic models.

The Aquatic Habitat Analysis and Visualization

Tool and database for the Finger Lakes

investigation are available on disk upon request.

To obtain a copy, contact the Information Transfer

and Media Services Group, National Biological

Service, Environmental Management Technical

Center, 575 Lester Avenue, Onalaska, Wisconsin

54650 (608/783-7550, extension 66).

References

Barko, J. W., R. F. Gaugush, W. F. James, B. J.

Johnson, T. J. Naimo, J. T. Rogala, S. J. Rogers,

and D. M. Soballe. 1993. Hydrologic

modification for habitat improvement in the

Finger Lakes: Pre-Project Report Number 2,

1993. U.S. Fish and Wildlife Service,

Environmental Management Technical Center,

Onalaska, Wisconsin; U.S. Fish and Wildlife

Service, National Fisheries Research Center, La

Crosse, Wisconsin; and U.S. Army Corps of

Engineers, Waterways Experiment Station, Eau

Galle Limnological Laboratory, Spring Valley,

Wisconsin, April 1993. EMTC 93-T002.

57 pp. (NTIS # PB93-181865)

U.S. Fish and Wildlife Service (USFWS). 1992.

Operating Plan for the Upper Mississippi River

System Long Term Resource Monitoring

Program. Environmental Management

Technical Center, Onalaska, Wisconsin,

Revised September 1993. EMTC 91-P002.

179 pp. (NTIS #PB94-160199)
REPORT DOCUMENTATION PAGE Form Approved

OMB No. 0704-0188

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1. AGENCY USE ONLY (Leave blank) 2. REPORT DATE

May 1995

3. REPORT TYPE AND DATES COVERED

4. TITLE AND SUBTITLE

Geospatial Application: Aquatic habitat analysis and visualization tool

5. FUNDING NUMBERS

6. AUTHOR(S)

Douglas A. Olsen

7. PERFORMING ORGANIZATION NAME AND ADDRESS

National Biological Service 

Environmental Management Technical Center

575 Lester Avenue

Onalaska, Wisconsin 54650

8. PERFORMING ORGANIZATION

 REPORT NUMBER

9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES)

National Biological Service 

Environmental Management Technical Center

575 Lester Avenue

Onalaska, Wisconsin 54650

10. SPONSORING/MONITORING

 AGENCY REPORT NUMBER

95-P006

11. SUPPLEMENTARY NOTES

12a. DISTRIBUTION/AVAILABILITY STATEMENT

Release unlimited. Available from National Technical Information Service, 5285 Port Royal Road, Springfield, VA 22161 (call

toll free 1-800-553-6847)

12b. DISTRIBUTION CODE

13. ABSTRACT (Maximum 200 words)

The Aquatic Habitat Analysis and Visualization Tool is a program and interface that allows users to view and create habitat models using the pre-improvement water quality

data collected for the Finger Lakes Habitat Rehabilitation Project (HREP). The Finger Lakes HREP is a hydrologic modification of a backwater lake complex in upper Pool 5

of the Mississippi River. The program and interface were implemented using Arc Macro Language and require the workstation version of ARC/INFO geographic information

system software (ESRI, Redlands, CA).

14. SUBJECT TERMS

GIS, ARC/INFO, AML, GRID, modeling, HREP

15. NUMBER OF PAGES

5 pp.

16. PRICE CODE

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 OF REPORT

Unclassified

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 OF THIS PAGE

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20. LIMITATION OF ABSTRACT
The Long Term Resource Monitoring Program (LTRMP) for the Upper

Mississippi River System was authorized under the Water Resources

Development Act of 1986 as an element of the Environmental Management

Program. The mission of the LTRMP is to provide river managers with

information to maintain the Upper Mississippi River System as a sustainable

large river ecosystem given its multiple-use character. The LTRMP is a

cooperative effort by the National Biological Service, the U.S. Army Corps of

Engineers, and the States of Illinois, Iowa, Minnesota, Missouri, and Wisconsin.