Part 2—Import, Animate, and Measure Sea Ice

Step 1 –
Launch ImageJ and Import the Sea Ice Data


harbour ith satellite dishes
Satellite dishes along the shore.
jason works at the computer
Downloading files at the local library computer.


Thanks to an efficient satellite connection to the Internet (and some nimble students), the team downloads the sea ice images to their local computers. They animate the images to show the changes in seasonal sea ice extents over the past 30 years and excitedly share what they see in the changing "seasons of ice." The elders in their village have said that in recent years, the ice is leaving earlier each spring and returning later each fall. The satellite images they see on their computers confirm native knowledge!
  1. Launch ImageJ by double-clicking its icon ImageJ Icon Small on your desktop (Mac or PC) or by clicking the icon in the dock (Mac) or the Start menu (PC).
    1. Launch ImageJ by double-clicking its icon ImageJ Icon Small on your desktop (Mac or PC) or by clicking the icon in the dock (Mac) or the Start menu (PC).
    2. When ImageJ is running, you'll see the tools and menus of ImageJ.
    3. annotated_tool-bar image J
  2. From ImageJ's main menu choose File > Import > Raw, then navigate (browse) down inside the folder of data until you see the monthly folder.
  3. Click once on the first file in the folder to select it, then click Open.
  4. In the dialog box that appears, set the fields as shown in the image below.

    Import_dialogue


    Some notes about importing sea-ice data sequences:

    • If you choose to explore sea ice images for the Southern Hemisphere, use a width of 316 pixels and a height of 448 pixels
    • All fields to be imported must be in the same directory or folder.
    • File names for the fields should be such that they are imported into ImageJ in the appropriate order: ImageJ reads in by alphanumeric order, so to import sequentially by time, the file names should have YYYYMMDD order for the date.

  5. Click OK and wait for ImageJ to import all 333 fields. This is a large amount of data so it may take a minute or so.
    On some computers, 333 fields or images may be too many for the available memory, and this could crash the computer. If you have limited memory, you may need to find another computer to use. Alternatively you can download and use the "quarterly" files.

  6. Save your stack by choosing File > Save As > Tiff... from ImageJ's menu bar. Name it sea-ice_extents.tif

Step 2 –
Apply a Color Scale (Look-Up Table) to the Images

The fields will come in as grayscale images. Adding a color scale that differentiates between ice and water will help you visualize the extent of the sea ice. To begin, you will download and apply a color scale (also called a look-up table or LUT) prepared by Dr. Walt Meier.

  1. Right-click (control-click on a Mac) on the link below and select the "Save link as..." option from the pulldown menu. Save the file to your Sea Ice folder or directory as a .txt file.
    Sea Ice Look Up Table (LUT) (Text File 4kB Jun21 07)

    Note: if this link opens into your browser, click your Back button and try again. You need to download the file to your own computer to use it.

  2. In ImageJ, select File > Import > LUT and navigate to where you saved the LUT file. Select the file and click open.
  3. The seaice_lut color scale shows a gradual change from blue (0% ice) to white (100% ice). Land areas are shown in green, coastlines are outlined in black, and areas where data are missingthe "pole hole" are gray.
    Stack with Color

    Creating a LUT—this is optional

    1. In ImageJ, an LUT is a 3x256 array of values between 0-255, stored as an ascii text file.
    2. The columns correspond to:
      • Column 1 = Red (R)
      • Column 2 = Green (G)
      • Column 3 = Blue (B)
      • 0 = no intensity, 255 = maximum intensity for the given color, e.g.:
      • RGB = 0,0,0 for white
      • RGB = 255,255,255 for black
      • RGB = 255,0,0 for red
    3. In Excel, you can create a LUT by putting numbers between 0 and 255 in three columns over 256 rows, then saving as a tab-delimited text file (comma delimited may also work). Save the spreadsheet as a .txt file and import it into ImageJ.

Step 3 –
Animate the Images

To get an overview of monthly sea ice changes, you will animate this stack of 333 satellite images to make a mini movie. This will allow you to review nearly 20 years of data in a matter of minutes. Enjoy the show!

  1. In ImageJ, start the animation by choosing Image > Stacks > Tools > Start Animation.

    • Image > Stacks > Tools > Stop Animation stops the animation.
    • Use Animation Options under the same pulldown menu as the start and stop animation, to control the speed, or use the "." and "," keys on your keyboard to move forward or back one frame at a time.
    • You could also choose to have the stack tools (see below for screen shot of stack tools) show up in the Image J toolbar. This will give you a controller for your animation.
    stacktools2
    Stack tools can be added into the Image J tool bar by holding down the red double arrow button at the end of the Image J tool bar for this drop down menu
  2. Watch the movie carefully enough to get a sense of the changes in sea ice over a single year. You can look at the file names in the upper left corner of the window to see what month is being displayed. Consider the following questions:
  3. You'll use a much smaller stack of images for the next part of the exercise. Just 28 images will be enough to do some measuring to document changes in the sea ice. If you like, you can save your large movie file by choosing File > Save As > Quicktime movie... If you choose this option you will need to save it as an "mpeg 4, normal quality."
  4. The ImageJ plug in that will allow you to save your animations as quicktime files can be downloaded from here Quicktime Plug in

Step 4 –
Consider the Polar Bear Dilemma in Churchill, Manitoba

polar bear and cub
Polar Bear and Cub waiting for sea ice to return. August 2007.


polar bear compound in churchill
Polar Bear "jail".


Churchill, Manitoba is on the western shore of Hudson Bay. It is home to a large population of polar bears. Myana and her classmates from Colorado want to know more about the polar bears. Susan and her students explain: "Polar bears need sea ice to survive—they travel over the sea ice to hunt for seals and other prey that live on the ice. Polar bears are good swimmers, but they need to have ice nearby to rest on or they can drown. Churchill is a region that is ice-covered in winter, but is ice-free through much of the summer. The polar bears must wait on land through the summer for ice to return before they can head out to hunt. They usually have to wait from July to November without hunting. That's why they get so hungry! During this time, they have to look for alternate food sources. This draws them into town and can cause trouble for everyone."
Downloaded from the Arctic Journal Website: Arctic Journal

Possible effects of climate warming on selected populations of polar bears (Ursus maritimus) in the Canadian Arctic / Stirling, I. Parkinson, C.L. Arctic, v. 59, no. 3, Sept. 2006, p. 261-275, ill., 1 map ASTIS record 59692

Polar bears depend on sea ice for survival. Climate warming in the Arctic has caused significant declines in total cover and thickness of sea ice in the polar basin and progressively earlier breakup in some areas. Inuit hunters in the areas of four polar bear populations in the eastern Canadian Arctic (including Western Hudson Bay) have reported seeing more bears near settlements during the open-water period in recent years. In a fifth ecologically similar population, no changes have yet been reported by Inuit hunters. These observations, interpreted as evidence of increasing population size, have resulted in increases in hunting quotas. However, long-term data on the population size and body condition of polar bears in Western Hudson Bay, as well as population and harvest data from Baffin Bay, make it clear that those two populations at least are more likely to be declining, not increasing. While the ecological details vary in the regions occupied by the five different populations discussed in this paper, analysis of passive-microwave satellite imagery beginning in the late 1970s indicates that the sea ice is breaking up at progressively earlier dates, so that bears must fast for longer periods during the open-water season.

Thus, at least part of the explanation for the appearance of more bears near coastal communities and hunting camps is likely that they are searching for alternative food sources in years when their stored body fat depots may be depleted before freeze-up, when they can return to the sea ice to hunt seals again. We hypothesize that, if the climate continues to warm as projected by the Intergovernmental Panel on Climate Change (IPCC), then polar bears in all five populations discussed in this paper will be increasingly food-stressed, and their numbers are likely to decline eventually, probably significantly so. As these populations decline, problem interactions between bears and humans will likely continue, and possibly increase, as the bears seek alternative food sources. Taken together, the data reported in this paper suggest that a precautionary approach be taken to the harvesting of polar bears and that the potential effects of climate warming be incorporated into planning for the management and conservation of this species throughout the Arctic.

As the research summary above shows, the formation of sea ice in November of each year is very important to the hungry polar bears around Churchill. In this section of the activity, you'll focus on Sea Ice conditions in November of each year.

  1. Make a new folder on your computer called November Extents
  2. Select and Copy all of the November files from the folder of monthly data you've been working with. You'll need all the files that have the number 11 after the year. For example, nt_197811_f07_v01_n.bin is the first file. Paste each one of the November files into your new folder.
  3. Though it's a valuable skill to be able to subsample a full dataset to produce a file that contains images from only one of the 12 months, this task has been completed for you for this example.

    Download a prepared stack ( 3.6MB Nov14 07) of the 28 November images.
    If you have problems with this link, here is a zipped version ( 709kB Nov14 07) of the file.
  4. When you're done, you will have 28 files that represent sea ice conditions every November from 1978 to 2005.
  5. In ImageJ, import the folder of raw November images into a new stack. Refer back to Step 1 above if you need a reminder of what you did. Do not add the LUT at this time.
  6. Save your stack. Choose File > Save As... > Tiff and give it the name NovemberStack.
November Stack screen shot NovemberStack, in grayscale

Step 5 –
Convert Ice Concentration to Ice Extent

The images you've been working with show ice concentration. In these, each pixel shows the amount of ice present in the area it represents, from 0 to 100 percent. Rather than estimating the amount of ice from concentrations, you'll convert the ice concentration images to show ice extent. To accomplish this conversion, we'll consider every pixel that has a concentration of at least 15% ice as ice-covered and areas with less than 15% ice as not covered by ice.

Why Measure Sea Ice Extent instead of Concentration?
From Ice Scientist Dr. Walt Meier

Sea Ice Extent is used instead of Sea Ice concentration for two reasons:

1. It makes for a simpler analysis. Every grid cell (pixel) in an extent image is either ice or no-ice. The total region covered by ice can be calculated by counting up all the ice pixels and multiplying by the area represented by each pixel (625 square km). If concentration were used, each grid cell would first need to be multiplied by its specific percent concentration to calculate the amount of ice.

2. For the satellite records from 1978-present, two different sensors were used. Their characteristics differ slightly, most notably for this discussion, in how near to the pole they can obtain data. The older sensor is not able to get any data north of 83 degrees latitude; the newer one can obtain data up to 87 degrees latitude. For the past 20 years, it is reasonable to assume that any region north of 83 degrees latitude is substantially covered with ice throughout the year. Thus, we can assume that the "pole hole" where the sensors do not obtain data is "ice-covered." This allows extent estimates to be continuous over the whole record. However, if concentration were used, we would not know the concentration of ice for areas in the "pole hole," so our record would be inconsistent.

The following pages from NSIDC explain more about the science of remote sensing of sea ice.

As discussed above, it is more appropriate to investigate extent, the region covered by at least 15% ice, instead of concentration. To convert to extent, you'll Threshold the image to select only those pixels with concentrations of ice from 15-100%. Thresholding highlights the pixels of interest in red.

    threshold_slider tool Threshold dialog box - drag the sliders or click the arrow buttons to set the threshold values
  1. Choose Image > Adjust > Threshold
  2. Pixels that have values between 38 (15% ice) and 250 (100% ice) represent ice covered pixels. Threshold the image to highlight values from 38 to 251. By using 251 instead of 250, you also select the pole hole region
  3. Do NOT click anything else in the Threshold window; simply close the Threshold window.

Step 6 –
Outline your Area of Interest - Hudson Bay

Map of the Arctic with villages of interest labeled. Map courtesy of Dr. Walt Meier
  1. Look at the map on the right to find the village of Churchill. As it is within Hudson Bay, you'll measure the extent of the sea ice within that entire bay on each of your November images. (click on the map for a larger version)
  2. Locate Hudson Bay on the map of your November Stack images.
  3. Select the polygon tool in ImageJ. On the first image in your November stack, draw a polygon around Hudson Bay. The boundaries of the region that you select do not need to be exact, but you will want to select all of Hudson Bay and avoid other ice water areas such as lakes.

  4. image J toolbar

    To make a Polygon selection single click on the Polygon tool (circled), return to your image and click around your area of interest. ImageJ will only analyze the pixels within your selection.



    November Stack with threshold and selection

    November Stack with thresholding applied and Hudson Bay selected. Once you have completed your selection you will have an outline around Hudson Bay as shown in this image. Be careful not to select areas too far from Hudson Bay where there are other lakes.



Step 7 –
Measure November Ice Extents

  1. To set ImageJ to record the measurements you want, choose Analyze > Set Measurements...
  2. Check the boxes next to Area, Limit to Threshold, and Stack Position. Uncheck any other boxes. Click OK.
  3. analyze_set_measurementsSet measurements pulldown and dialog box
    set measurements window
  4. Choose Analyze > Clear Results to delete any previous measurements from the Results file.
  5. Choose Analyze > Measure to have ImageJ count and record the number of highlighted pixels inside your selection.
  6. Advance to the next slice in the stack using the ">" (period) key on your keyboard, then press "alt-M" (command/Apple M on a Mac) to record the measurement. Continue measuring for each image in your stack. Each measurement you make will generate a new row in the Results table. Note: Don't worry if you measure an image twice, this can be cleaned up in the next part of the process.
  7. When you have measured all 28 slices, save your Results so you can bring them into Excel for graphing.

  8. Click your Results window to make it active. Choose File > Save As... > Results...and enter .xls as the file extension for spreadsheet.
  9. Name your new file NovemberResults.xls and click Save. Save it in your Sea Ice Folder.
  10. Save your stack again, just in case you need to go back to it.

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