Dr Jambone’s Guide to OceanView Bliss (feat. the Jaz)

There comes a time in every sensory ecologists life when the sudden desire to measure spectral reflectance arises. In such fits of whimsy it oft becomes necessary to use a particular program to quench thine spectral thirsts; OceanView (Ocean Optics). After downloading said program, paying the not insignificant licence fee and downloading spectrophotometer drivers, finally opening OceanView only to be confronted with an array of obscure icons and menu options can set even the most steely of ecologists into a fit of the vapours. As such I have put together a brief step-by-step guide to getting started with spectral reflectance measurements using OceanView and a Jaz spectrophotometer that even a mere layperson could follow.

oceanview-01-wizard_categories

Step 1- Setup

  • Plug the Jaz’ USB Cable into the computer and get your probes set up
  • Turn on Jaz
  • Open the OceanView program
  • If Jaz does not appear under ‘Data Sources’ you may need to ‘Rescan Devices’ or try closing and opening the program again. It may also mean that your computer does not have the drivers necessary to run the spectrophotometer (http://oceanoptics.com/product-category/drivers/).

 Step 2- Enable strobe using the Jaz unit.

  • Press red (X) button
  • Arrow down to ‘PX lamp’ press the green (P) button.
  • Select ‘Setup’ (#)
  • Select ‘Timing control’ (#)
  • Arrow down to ‘Free Running’ press the green (P) button
  • Select ‘Enable’ (∆)
  • Press (X) button
  • Press (X) button again
  • Select ‘Enable Strobe’ (∆)

You will see the light coming out of the probe, if its flashing try again and make sure the ‘Free Running’ option is selected.

Step 3- Ocean View

  • In OceanView select ‘New Spectroscopy Application’ or ‘Run a Wizard’ depending on version
  • Select ‘Colour’
  • Select ‘Percent Reflectance Processing’
  • Next is where you set up your measurement parameters. These will differ depending on your study design and setup. For example my last experiment had integration time = 40msecs, boxcar = 10 and Average Scans = 5. Other options here can be left at their default settings. As a guide set your integration time so that the peak of the intensity counts (red line on the right hand side) sits somewhere around 30,000. Once you’re ready click ‘Next’.
  • Calibrate your white standard – place your white standard against your probe and click the lightbulb icon. Click ‘Next’.
  • Calibrate your dark standard – Place your dark standard against he probe. If you wish to disable the strobe for your dark standard you can do so with the tick box down the bottom left. Click the lightbulb icon. Remember to turn your strobe light on again and then click ‘Next’.
  • Choose which delightful graphical representations of your data you would like to see. If you just want spectral curves then don’t worry about any of these options. Click ‘Finish’.

Step 4 – Taking measurements

  • Set up your file directory – Click the icon that looks like a piece of paper with a wrench next to it. This step will send all of your saved spectra to a single folder and automatically assign file names.
  • On the left hand side set your target directory folder and basename of your files. I also like to use the file counter option rather than the time stamp.
  • On the right hand side select ‘Save every scan’
  • Set ‘Stop after this many scans’ to 1.
  • Click ‘Apply’ and click ‘Exit’

You’re now ready to start measuring your animal/vegetable/mineral. Place your specimen against the probe (or vice versa) and click the ‘Save graph to files’ icon. Your files should appear in your file directory and will be numbered consecutively!

 

Sincerely,

Dr Jambone

 

P.S. Here’s how to use the Jaz on its own if you like…

Using the Jaz on it’s own

Step 1- Turn it on!

 Step 2- Enable strobe using the Jaz unit

  • Press red (X) button
  • Arrow down to ‘PX lamp’ press the green (P) button
  • Select ‘Setup’ (#)
  • Select ‘Timing control’ (#)
  • Arrow down to ‘Free Running’ press the green (P) button
  • Select ‘Enable’ (∆)
  • Press (X) button
  • Press (X) button again.
  • Select ‘Enable Strobe’ (∆)
  • Press home button to return to main menu.

Step 3- Settings

  • Select ‘Tools’ (O)
  • Select ‘Manual Control’ (∆)
  • Select ‘Acq. Parameters’ (∆)
  • Select ‘Integration Time’ (∆)
  • Select ‘Manual’ (#)
  • Use arrows to set integration time (e.g. 40msec) and press green (P) button
  • Select ‘Boxcar’ (#)
  • Use arrows to set boxcar (e.g. 10) and press green (P) button arrows

Taking measurements

  • Press home button to return to main menu
  • Select ‘Reflectance’ (#) to do colour measurements
  • This will begin scope mode
  • Take a measurement of your white standard with the (triangle) button
  • Take a measurement of your dark sample with the (#) button
  • Begin measuring your sample with the (O) button. Sometimes it asks if you want to adjust to light, this will change your manual settings so best not use it.
  • Press the yellow disk button to save your spectra.

You will need a card reader to get your spectra off the memory card and onto your computer. The jaz saves things in weird file types with 5 columns that can be opened as a text file. The first column is the light spectrum, the fifth column is your reflectance data.

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