Lihdat Manual for Lihdat (single sample

processing)

Startup Launch Matlab

Type “lihdat” in the command window and hit enter. This will launch lihdat.

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

Startup Click on “Setup 1 Sample”

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.

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.

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.

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.

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

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

Classifying ROIs You must close microsoft excel if

you are looking at the classified data file already.

Type “do_everything”in Matlab window

Classifier

Sample metadata comma delimited and can be imported into excel. The metadata file is located:

F:\data\lihdatlogs\one_sample_datasummary\one_sample_datasummeries.dat

Example: #fields:

samplecode,sample_date,sample_time,site,water_col_pos,sample_label,orig_volume,temp,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_datasummeries_classified.csv

Collected Data

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.