Quest 2006, Benthic Photographic Processing & Analysis, Jennifer E. Smith

Benthic Marine Photographic Processing and Analysis

Step #1.

Photographic Editing

1. Plug your camera into your computer using the USB cable (lower right side of camera)

2. Turn your camera on and make sure the main setting is on the “view pictures” mode rather than the “take pictures” mode (turn the dial on the upper right to the  play button)

3. Open up “My Computer”

4. Double click on the USB drive-probably “E://”

5. Make sure the folder contains your pictures (go to “view”—Thumbnails); if your pictures are not there ask a faculty member to help

6. Copy the entire folder to your desktop and label the folder “QUEST06 Team #__”

7. Open up Photoshop (go to Start-Programs-Adobe-Photoshop)

8. Now open up your pictures (file-open-browse to your pics and open, you can hold down the shift key to select and open many multiple pictures at a time)

9. Check to see if your quadrat perfectly centered in the picture? If not, go to “Image” “Rotate Canvas” “Arbitrary”. You can try different degrees of rotation until you are satisfied. I would suggest starting by entering 1 or 2 and adjust the clockwise/counter clockwise setting depending on which direction you want to rotate the picture.

10. Make sure the tool bar is visible in Photoshop (go to “Window”-“show tools”)

11. Using the upper left tool on the toolbar (Rectangular Marqee tool) highlight your picture so that you leave just a small portion of the quadrat behind then go to “Image” then down to “Crop”

From this:To this:

12. Now you can adjust the lighting on your picture to either make it darker/lighter and/or adjust the contrast. To do this go to “Image” “Adjust” ”Levels”, click on “Auto” and see if you like the results, if not you can move around the arrow in the middle of the chart: left to right and see how it changes your picture. Ideally you want to be able to see into the dark areas of your picture without overexposing other areas. Next you can go to “Adjust” “Auto Contrast”.

13. Your picture should look pretty good at this point, if not ask a faculty member for help.

14. Save your picture with the following code: Team_isobath_random number in the same folder that your un-edited pictures are in.

Step #2.

Photographic Analysis

  1. Open Photogrid 1.0 beta. “Start” “Program Files” “Photogrid 1.0 beta”
  2. Go to “Options” “Preferences” now find the “button file and path” and click on the blank button at the far right of the screen and select the “quest 06” button file, then click “Apply” and then “Close”
  3. Now in the Photogrid program you should see all of the species codes appearing at the bottom of the screen in the various organism categories-coral, algae, invert, other
  4. Now click on the “Open” button in the lower left area of the screen
  5. Browse to your first picture, click “open”
  6. Now find where it says “# Rand Pts” and change the value to 50
  7. Now click on the “Rand Pts” button and you will see that random points will have magically appeared on your photo
  8. Now click in the box next to the number 1 on the left side of the screen, you should see that the #1 on you random points has changed from red to yellow. To zoom in and get a closer look to identify what #1 is in your photo, just left click on the picture and it will automatically zoom in on the point you are working on; to zoom out just right click on the picture and it will automatically zoom out.
  9. Once you are happy with the degree of zooming, decide what organism is under your random point and find that organism’s code in the buttons at the bottom of the screen-click on the button. Now the program will automatically jump to the next random point and continue until you have gone through all points.
  10. If you are unable to identify an organism, ask a faculty member to help. There is a category “Black hole” which is specifically for points which are placed over dark areas in your photograph. Ideally you want to avoid identifying points as black holes because it reduces the amount of “real” data that you have. To deal with this you can either reopen your picture in photoshop and adjust the lighting or you can try to use the brightness and contrast bars in Photogrid.
  11. When you are done with all 50 points the program will say “All Done!”
  12. If you ever come across an organisms that isn’t in the button options you can type a name into the box but just MAKE SURE that you put 3 COMMAS after the organism name; if you don’t do this Photogrid will not export your data.
  13. After you have gotten the “All Done” message click on the “Save” and then “Export” buttons
  14. Now you can simply click on “Next Pic” and Photogrid will automatically open the next picture in your folder.
  15. Continue until all pictures have been analyzed. Don’t forget to click SAVE and EXPORT after EACH PICTURE.

Step #3.

Data Analysis:

  1. Open Excel
  2. Go to “File” “Open” and then browse to C:// Program Files/ PhotoGrid 1.0/ Photogrid Data and open the most recent Excel File.
  3. The file will have several columns that we don’t need so Copy the column that says Pic Name into another worksheet and paste it into the first column. The go back and find the column that has all of the species names in it-copy that column and paste it into your new worksheet right next to the picture name column. You should have several hundred entries-each corresponding to a random point.
  4. Go to “Data” “Pivot Table and Chart”, click “Next”, highlight your 2 columns.
  5. Click “ New Worksheet”
  6. An empty table will open up. Click and drag the “Pic Name” button over to the left side of the blank table. Click and drag the “Species Name” button over to the top panel in the table and finally click and drag the “Species Name” button into the middle body of the table. If all goes well…you should have data.
  7. It is difficult to manipulate data in a Pivot Table so I usually copy and paste everything over to a new sheet.
  8. Since we only analyzed 50 Points in Photogrid we now need to convert these points into percent cover. To do this each column needs to be multiplied by 2-you can do this either in Excel or Minitab-whichever you prefer.
  9. Once your data are in Percent Cover format you are ready to begin looking at descriptive statistics… Data are cool!

* Now Find the QUEST PIX Folder on your Desktop and practice on the 2 photos. Get used to the button file and use the Key (see following pages) if necessary.

Species Key for Photogrid Button File QUEST 2006

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Quest 2006, Benthic Photographic Processing & Analysis, Jennifer E. Smith

CORAL

" Porites compressa , "Por com"

" Porites lobata , "Por lob"

" Porites evermani , "Por ev"

" Porites rus, "Por rus"

" Montipora capitata, "Mon cap"

" Montipora patula, "Mon pat"

" Montipora flabellata, "Mon fla"

" Montipora sp., "Mon sp"

" Pocillopora meandrina, "Poc mea"

" Pocillopora damicornis, “Poc dam"

" Pocillopora eduxii, "Poc edu"

" Pocillopra ligulata , "Poc lig"

" Pavona varians, "Pav var"

" Pavona duerdeni , "Pav due"

" Leptastrea purperata, "Lep pur"

" Leptastrea bottae, "Lep bot"

" Tubastrea coccinea, "Tub coc"

" Cyphastrea occellina , "Cyp oc"

" Leptoseris incrustans, "Lep inc"

" Fungia scutaria, "Fun scu"

ALGAE

" Turf, "Turf"

" Crustose coralline,"CCA"

" Halimeda opuntia, "Hal op"

" Caulerpa racemosa, "Caul rac"

" Caulerpa serrulta, "Caul ser"

" Caulerpa sertulariodes, "Cau sert"

" Dictyosphaeria cavernosa, "Dict cav"

" Dictyosphaeria verslusii, "Dict ver"

" Codium arabicum , "Cod ara"

" Neomeris annulata, "Neom an"

" Ventricaria ventricosa, "Ven ven"

" Lobophora variegata , xData1"Lob var"

" Turbinaria ornata , "Turb or"

" Padina sp, xData1, "Padina"

" Dictyota sp, xData1, "Dicty"

" Sargassum sp, "Sarg"

" Galaxaura marginata, "Galax"

" Asparagopsis taxiformis, "Asp tax"

" Gibsmithia hawaiiensis, "Gib haw"

" Pradea weldii, xData1, "Pra wel"

" Dasya irridescens, "Dasy ir"

" Martensia fragilis, "Mar frag"

" Neomartensia flabelliformis, "Neo fla"

" Portieria hornemanii, "Por hor"

" Cyanophyta , "BG"

" Other, "Other"

INVERTS

" Tripneustes gratilla, "Trip gr"

" Diadema paucispinum, "Dia pau"

" Echinothrix sp, "Echinot"

" Echinometra mathei, "Ech mat"

" Echinometra oblonga, "Ech obl"

" Heterocentrotus mammillatus, , "Het mam"

" Chondrocidaris gigantea, "Chon gig"

" Colobocentrotus atratus, "Colo at"

" Acanthaster placi, "Acan pla"

" Linkia multiflora, "Link mul"

" Ophicoma spp, "Ophic"

" Actinopyga mauritiana, "Act maur"

" Actinopyga obesa, "Act obe"

" Holothuria atra, "Hol atr"

" Holothuria whitmaei, "Hol wit"

" Ophiodesoma spectabilis, "Oph spec"

" Spirobranchus giganteus, "Spi gig"

OTHER

" Quadrat, "Quad"

" Black hole, "Bl hole"

" Sand, "Sand"

" Limestone, "Limest"

" Basalt, "Basalt"

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