The GIS program that simulates habitats,
integrating high quality imagery and analytical tools.


Click here to view the Quick Start Guide in pdf form and save it on your computer.

Click here to view the Reference Manual in pdf form and save it on your computer..

EASy Quick Start

Your Users Guide to

Pelagic Habitat Analysis Module

Software for the Study and Management of Pelagic Species

Table of Contents

Using PHAM Quick Start

Installing PHAM

Creating a New Project

Editing Map Display

Importing Data

Displaying Data Blobs

Spatial Analysis

Importing Imagery

Displaying Imagery

Creating Plots

Running Simulations

Exporting Data & Maps

Using PHAM Quick Start

PHAM Quick Start is a simple, easy to use guide to get you started in PHAM. The detailed instructions, answers to frequently asked questions, examples, and common mishaps make it even easier to learn and use PHAM. In addition, there are links on each page to even more information for the advanced user!


1.Using the Table of Contents,
    click on the desired chapter

2. Follow the "Step-By-Step" Instructions

3. Read through the Frequently Asked
    Questions, FAQs section

4. Make sure to avoid the common mishaps
    in the "Common Mistakes" section.

5. Check out the Reference Manual cited by Appendix Letter

Where can I download
    the Reference Manual?

The Reference Manual can
be downloaded at the top
of this page by clicking
on the word "here".

What if the information in
    Quick Start, Reference
    Manual, demo and example
    wasn’t enough to solve my

Please check the User Forum
on the "Users Group" page first.
If the problem is still not solved
then email us through the
"Contact Us" page.


Skimming: Please read the Quick
    Start instructions carefully.

Doing without understanding:
    When following the steps,
    if there is something you
    don't understand, please refer
    to the Reference Manual.

For more information, see Reference Manual Appendix A: PHAM Basics

Installing PHAM

PHAM provides researchers with the tools to examine data in a 4 dimensional context – latitudinal, longitudinal, vertical, and temporal (Ref Manual Appendix A). This unique GIS program contains an interface for satellite imagery products from NASA and others. PHAM runs on Windows Operating Systems.


1. Select Download Program from the menu.

2. Check that your computer meets the
requirements specified in the box to the

3. Register as a user with a valid email
and affiliation and click Submit. This
should result in the screen below:

4. A temporary password will be sent to
your email. Copy and paste this
password into the "Password" box
and click "Download"

   5. Change the temporary password
   to the password of your choice by
   clicking the "Change Password"

   6. Click on the PHAM Lite Program
   Link and follow the instructions.

   7. Optional: Return to the website
   and click on the PHAM Lite Demo link
   to download the demo.

For more information, see Reference Manual Appendix A: PHAM Basics

Creating a New Project

Whenever you start a new study, you will want to start a new project as well. By creating a new project, your work is kept organized with a new subdirectory complete with a separate database designated to your next study. The folder and database created will have the same name that you give your project.


1. Double click the PHAM icon

    located on your desktop
to start up PHAM.
3. Type in the name of your new project and click Ok.

2. Choose File New.
(Ref Manual Appendix A).


Can I keep imagery from
   a previous project?

Yes. If you would like to use the
    imagery from a previous project,
    do not create a new project, but
    rather go to File-Save As and
    check the box next to Clear

Can I use symbols
   in the project name?

You can use any symbol except
    a period or a backslash.

Unoriginal project naming

Using the same name as
    an older project will result
    in the loss of the older project

For more information, see Reference Manual Appendix A: PHAM Basics

Editing Map Display

The following steps guide you through changing the zoom, projection, grid lines, grid labels, and the units of the map. PHAM has options to change the extents of the map as well as the grid lines and projection type.


1. To change the screen extents or map center, use the buttons on the main toolbar (Ref Manual Appendix E.1).

2. To change any other map options go to View in the main menu. Then click on Display Settings.

3. Once in Display Settings, click on the Settings tab.

4. To change the projection, choose the projection type from the Projection drop down menu

5. To turn grid lines/labels on or off, check or uncheck the box next to Grid Lines or Grid Labels

6. To change the units of the map, click select from the Distance drop down menu and the Lat/Lon drop down menu.

For more information, see Reference Manual Appendix B.1.1: Map Settings

Importing Data

PHAM is equipped with an easy to use database wizard that imports your data and stores it in the project database. Following the steps is very simple, but make sure you look at the appendix on this one! Understanding the data fields is essential to analyzing your data properly in PHAM.



  1. Create a comma separated values (.csv) file with the following format and columns and transfer your data into the appropriate columns (Ref Manual Appendix C). Necessary data fields include: Latitude, Longitude, and date/time fields. Order is not important, but the column headers should all be present and these headers must be in the format shown below.

  2. Back in PHAM, choose File-Import- Measurements-Database Wizard
  3. Click on Source File. Browse to and select your data file. Then click Process.

If not all your data was imported successfully…

- Choose Edit-Project Database.

- Select the VDB Errors table from the side panel. Scroll to the Error Reason column to see why your data were not imported.

- Fix errors in data file.

- Repeat Steps 2-3.

Can I leave any data
   columns blank?

Station, sample, and voyage
    can all be left blank.
    PHAM will assign unique
    identifiers for these columns.

What type of characters
   does each field accept?

Voyage, Station, Sample, Units,
    and Measurement Type can
    accept text and characters;
    while all the other fields
    must be numeric.
    For further help with this please
    refer to Appendix C for examples.


Duplicate Records: PHAM will not accept
    records where the voyage, sensor,
    date, location, depth, measurement
    type, and measurement value are all
    the same.

Invalid Dates: PHAM accepts dates in the
     format “mm/dd/yyyy hh:mm:ss” Be
     sure to check that you have your dates
     in this format.

Incomplete Records: Every record must
    contain a date, longitude, and latitude.

Different Locations, but Same Station Name:
     Take care not to name two different
     locations the same station
     name… This will result in
     only the first station's data
     to be imported.

Poor Planning: Take the time to
    understand the data
    structure by reading
    Appendix C. This will save
    you a lot of time in the long

For more information, see Reference Manual Appendix C: Understanding the Data Fields

Displaying Data Blobs

Once the data has been imported into PHAM, it can be displayed as circles, filled in dots, or pies. The value placed on each station can be a count, sum, average or presence/absence. As always the steps below will help guide you through the process, but be sure to consult the references if you lose your way.



1. Within PHAM, select View-Display Graphics
    and then click on the Blobs tab (see below).

2. To Select Data to display: Click on the box next to
    the Measurement Type name in the Blob Type box.

3. Select the Value to Display in the Type dropdown

4. To change the color of the blobs. Click on the Pen and Fill color
    boxes next to the measurement type and select the desired

5. For station locations, select the box next to All
    for all stations or Active for stations sampling in
    timestep (if running simulation).

6. For solid blobs click on the Solid button.

7. To change the size of the blobs, increase or decrease
    the number in the Count box.

To Define Scaling of Blobs, Select the "Shape" Box.

- Click on the Measurement Name in the Blobs Type box (see above).

- Select a Shape Type from the drop down box and choose Add. This adds a bin for the measurement type.

- Specify the Range value, Size and Color for the bin.

- Click the box directly to the left of the left of the blob type name to make the respective bin visible on the map.

For more information, see Reference Manual Appendix C.3: Data Graphics

Spatial Analysis

The Spatial Analysis tool allows you to match up your data with imagery. Within this tool you can look at correlations between your data and the imagery and export the matched data to a csv file.



1. Select View-Spatial Analysis Options.

2. Under the Measure tab, select one or more
    Categories (typically your measurement types)
    and click Read.

3. Add Characteristics (typically imagery) to match to
    the categories by clicking Add in the characteristic

4. Specify the bins of the Characteristics in the boxes
    next to min, max, and number of bins

5. Click Ok.

For Density & Correlation Plots:

- The Density tab governs what variables appear in the Sample Density Plot.
Once you've run the spatial analysis, you can choose which Characteristics you would like to plot.

- The Correlation tab governs what variables appear in the Characteristic Distribution / Correlation Plot. You can choose to plot this as a false color image, with confidence intervals, and/or on a reverse axis.

For more information, see Reference Manual Appendix E: Spatial Analysis

Importing Imagery

After your measurements have been loaded into your project, you'll want to get the environmental data that correspond to your dataset. Satellite imagery is available in more formats than there are sources. PHAM has the ability to read many of these imagery formats. Beginners should start with the imagery available on the imagery page. If you want to try your own imagery, be sure to read Appendix D.



1. Browse to the imagery page on the website.

2. Download any desired Imagery to a local folder.
    Imagery must be uncompressed and placed
    in one folder on the computer
    (Ref Manual Appendix D.1)

3. Back in PHAM, choose

4. Select the Category that corresponds to the
    downloaded imagery (Ref Manual Appendix D.3).

5. Click the Add Dir button.

6. Browse to the location of the downloaded
    imagery files and double click one of the files.

7. Click the Scan button.

8. Highlight the imagery files to import.

9. Click OK

For more information, see Reference Manual Appendix D.1: Import

Displaying Imagery

These steps will guide you through browsing through images and setting up a scale for your imagery set.



  1. Within PHAM, select Process-Browse Images.

  2. Select an imagery set and date from the Browse Images Toolbar

  3. To change the scaling, select View - Display Settings then click on the Categories tab.

  4. Select the imagery to be scaled then click the Edit button.

  5. To change the scaling, use the formula in the Function box.
    • Off variable (offset) = number in the leftmost box directly below the function box.

    • Slp variable (slope) = number in the second to the left box directly below

    • Physical maximum and/or Physical minimum = maximum and minimum values of the imagery parameter

    • Pixel value = the pixel count that corresponds to the desired maximum or minimum value.

    • Plug the values from a-c and solve for the max. and min. pixel values

    • Place the result for the min in the box denoted by (*) and the result for the max in the box denoted by (!)

  Displaying Imagery - Changing Palettes:

These steps will guide you through changing the palette for your imagery.



1. With an imagery set displayed on the screen, right click anywhere on the map and select Palette.

2. The top drop down box contains a list of pre-set palettes for the different imagery types. To try one of these simply click on the name of the palette and click Ok.

3.If none of the pre-set palettes work, use the advance options to create your own palette. Doing this ensures that the pre-set palettes remain unchanged.

4. Click on the black arrows, continue holding down while you move the arrow up or down along the scale.

5. To change the color of the post, simply double click on the arrow and select the new color box. Then click Ok.

6. The values on the side of the colorbar can be set to read either the pixel value or the physical value by toggling the Pixels or Units button at the top of the color bar.

For more information, see Reference Manual Appendix D.2.1: Palette

Creating Plots

With PHAM, you have the ability to create interactive plots of the data and imagery by following the simple steps below.



1. Within PHAM, select View-Data Graphics
   and then select the Plots tab.

2. Click on the names of the desired plots.
   Then click Ok.

3. Select data to include in the graphs by clicking,
   pressing shift, and then dragging to another location
   on the map.

Basics on the Plots Available:

  • The plots will show the y-variable with respect to the distance from the first point to the second point on the drawn line.

  • Depth Profile – plots the depth of the data across your transect

  • Image Statistics/Profile – plot results from spatial analysis of selected imagery

  • Characteristic Distribution/Correlation - plot results from spatial analysis of data

  • Sample Density Probability - plots results of spatial analysis density predictions.

For more information, see Reference Manual Appendix C.2.3: Plots

Running Simulations

Simulations are videos of the data and/or an imagery set through time.



1. Select View-Display Settings.

2. Click on the Simulation Tab

3. Type in the start date in Simulation Start and the
    end date in Simulation End

4. Type in the Number and Units of the time step in
    Display Delta. Then click Ok.

5. If you would like to display an imagery set, select
   View-Data Graphics. Click on the Images tab.

6. Then select the desired imagery set from the first drop down box. Then click Ok.

7. Select Process-Simulation Controls.

8. Set the Retain Days to the number of days the program
   should look forward or backward for satellite imagery.

9. To control the simulation click the buttons indicated below.

For more information, see Reference Manual Appendix D.2.3: Simulations

Exporting Data & Maps

One of the greatest things about PHAM is its compatibility with the programs most scientists already use. All data and maps generated in PHAM can be exported in a variety of formats simply by following these steps.



For Data

1. Select View-Spatial Analysis Options.

2. If spatial analysis has already been run,
   then click Export.

3. Select the variables to export

4. Click OK.


For Maps

1. Select File-Export-View

2. Choose File Type in the Save as Type

3. Click Save

For more information, see Reference Manual Appendix A.4: Export Capabilities