1. Lihdat  Manual for Lihdat (single sample processing)

2. Startup  Launch Matlab  Type “lihdat” in the command window and hit enter. This will launch lihdat.

3. Sample Setup  Connect your inflow and outflow lines to a funnel.  Pre-screen your sample before adding it to the funnel. You will be prompted at the end of lihdat processing to enter the volume you put in the funnel. Automatic stirrer

4. Startup  Click on “Setup 1 Sample”

5. Startup  You can flush and backflush without recording data using the specified buttons.  It is recommended to flush with filtered sea water before processing your sample.  You should also perform a flush containing your sample to insure the first recorded data has an accurate density of your sample.

6. Startup  Enter your sample information  Once entered, hit START This value is critical to getting an accurate density calculation. It is the volume swept to collect this sample.

7. Running the sample  You will see messages in the status window displaying the processing sequence.  A window will pop up asking to start the sample. Click Yes, continue if you have sample in the funnel.

8. Running the Sample  The strobe will launch.  Two separate windows should launch to segment the ROIs. They will close automatically at the end of processing.

9.  Once a stable average density has been calculated (threshold is standard error <.03). Your sample is done processing.  You will be prompted to enter the lihdat sample volume. This is the volume in your funnel, NOT the volume swept to collect the sample originally.  You will be asked to classify the last sample. If you choose “No” you can always process it later. Running the Sample

10.  The outputs of lihdat are “ROIs” (Regions Of Interest) along with metadata and density calculations.  ROIs are recoreded into folders based on the time they were collected, for example: F:\data\lihdat\y2010\d095\h15\ roi.56074875.00.tif Collected Data

11.  Classifying ROIs  You must close microsoft excel if you are looking at the classified data file already.  Type “do_everything”in Matlab window Classifier

12.  Sample metadata comma delimited and can be imported into excel.  The metadata file is located: F:\data\lihdatlogs\one_sample_datasummary\one_sa mple_datasummeries.dat Example:  #fields: samplecode,sample_date,sample_time,site,water_col_pos,sample_label,orig_volume,te mp,sample_valve,num_subsamples,first_roipath,last_roipath,numrois,mean_subsample _density,std_subsample_density,num_subsamples,sample_site_density  20100330135635, 2009/07/15, 12:00:00, Menemsha, water col pos, mememsha_5, 77754.42, temp, 7, 22, F:\data\lihdat/y2010/d088/h13/roi.50260250.00.tif, F:\data\lihdat/y2010/d088/h14/roi.51355343.00.tif, 260, 0.23636, 0.13574, 22, 0.00030399  Metadata for each subsample processed for your sample is at: F:\data\lihdat\logs\one_sample_datalogs\  The classified data for ROIs has the same format with added identification data.  F:\data\lihdatlogs\one_sample_datasummary\one_sample_datas ummeries_classified.csv F:\data\lihdatlogs\one_sample_datasummary\one_sample_datas ummeries_classified.csv Collected Data

13. Troubleshooting  If pump is no longer working  Check to make sure all ports are plugged in on the side of the laptop.  You may hear the valves switching while the pump is not working  Press the reset buttons “1” then “2” on the side of the pump pictured below.