Platform SOP

Standard Operating Procedures

TRACKING PROCESS

  1. Tracking animals will be done primarily through the click detector. Once you see a click train (3-5 consecutive clicks along the same bearing), start a detection in the Detection tab. Hit F1 to enter the time & date. Hit F1 to enter the Lat/long. Enter the Acoustic ID # along with at least the initial bearing angle. You can fill out the other fields as the event goes on. There are 3 Detection tabs so that you can track 3 things at once. You can also use the TD tab to localize whistles.

    1. For encounters in which there are both bearings from the whistles and clicks, you can merge them into one event by going to the map, holding down CTRL + left click and select “Assign X bearings to UID#”. You should then see both the whistle and click bearings as the same color. You may need to repeat this step over the course of the encounter.

  2. A mark should be placed at the start position on the trackline of the initial bearing location- clicks don’t stay on the map for long, the markers will last longer. Double click the spot on the map to enter “start of A#- [species]”

  3. Measuring the perpendicular distance from the ship’s track to the marked location can be done in the Map tab, by double-clicking next to the map comment and click + hold to the convergences (note: if you happen to select the pixel the map comment is on Pamguard won’t draw the measuring line). If you have R and L locations, measure on both sides of the ship’s track and take the average distance (this will be the beam distance). If you only have one location, take all measurements from the trackline to that location. Also measure the distance from the ship’s track along the first angle plotted that converged at the location (the first detection distance).

  4. Can you tie this detection to a visual sighting?? If so, be sure to record the visual ID, and any other info from the visual team in the comments field (time, bearing, distance, species ID, etc.).

    1. Use the Visual to Array Angle module and the incoming information from the flying bridge to do so

  5. For marking the end of a detection, follow these general guidelines

    1. Sperm whales: until 5 min have passed where no clicks are detected (can feel free to press F1 prior to this but keep the detection tab open for another 5 min)

    2. Beaked whales: get an end time when 1 minute has passed without clicks. You will probably need to press F1 a few times as the clicks come back (thus constantly updating the end time)

    3. Dolphins: if it’s just clicks, the end time is within 30s of the last click train. If it’s whistles and clicks, keep the detection open for up to 2 min after the last whistle. It’s common for whistle presence to come in and out

  6. Click “Save” to save this detection to the database.

    1. If you end the encounter prematurely, you can double click on the row below the form to make any changes. Note that the F1 features do not work in this view. If the encounter’s row is not visible, you can make a comment using an asterisk (*) in the User Input for later modification during the QAQC process.

  7. Look/listen for new groups. Continue to check bearings to sounds. Sometimes you will pick up a new group ahead of the ship while you are still hearing a group behind the ship.  Start a new Acoustic ID when another group is detected.  If a second group is detected before you have stored the info about the first group, you can save the first group and start a new group, then go back and edit the info for the 1st group when time allows.  Make note if long periods occur with no acoustic activity (i.e. “AQ”).

<<<<<<< HEAD For further details, please refer to the [movie link- TBD]

DATA QAQC & BACKUP

Tracking Computer

  1. Clean up edits at the end of each day

    1. Open SQLiteStudio from the task bar (silver icon)

    2. Look at tables for current cruise Leg

    3. Tables to check are Detection (1,2,3), Effort, Sperm whale, UserInput, Map comments

      1. Open table (double click), then select the Data tab

      2. Scroll to bottom and/or advance page to end for latest data entries

      3. Detection (1,2,3): Use notepad ID numbers to check AC_ID count and all relevant fields. Where localizations were impossible, the entry should have NA

      4. Sperm whale: should have at a minimum a start and end time, start and end lat/lon, click types heard/seen, and estimate of number of animals in the comments field

      5. To edit a field - double click and it will turn blue, click once more in the field, then the cursor will appear and you can edit. Click on the GREEN check box to commit the edit. Click the RED X if you want to restore the field to its original value.

      6. R-Click on lower bar and select Close all windows

    4. Make sure all fields are filled in and Acoustic ID numbers have not been skipped

    5. * in front of any comment signifies a correction is needed

      1. Add (DONE) to the beginning of all * fields that have been corrected

  2. Insert NEFSC_48 hard drive into computer

  3. Go to E:\AMAPPS 2025 Backup\Pamguard_Binaries_Databases

    1. Make copies of the day’s database with the date (ex. NEFSC_NE-OFFSHORE_20250110_PC2501_Leg1_Tracking.sqlite3)

    2. Copy the days Binary files, and Database to Acoustics NEFSC_48 hard drive under the respective computer’s folder

  4. Update daily summary of acoustic detections NEFSC_NE-OFFSHORE_202501_PC2501_Acoustic-Detection-Summary

    1. Backup to the external hard-drive under Cruise_Summary

  5. Update daily notes in the cruise log PC2505_Leg#_PAM_Cruise_Log 

    1. Backup to the external hard-drive under Cruise_Summary

  6. Save daily print screen power point 

    1. Backup to the external hard-drive under Daily_Printscreens

  1. Recording Computer

    1. Go to E:\AMAPPS 2025 Backup\Pamguard_Binaries_Databases

      1. Make copies of the day’s database with the date (ex. NEFSC_NE-OFFSHORE_20250110_PC2501_Leg1_Tracking.sqlite3)

      2. Copy the days Binary files, and Database to Acoustics NEFSC_48 hard drive under the respective computer’s folder

  2. TerraMaster

    1. Check that the internal hard drive has enough space for the next day; change drives if they will run out of space.

This will need to be moved to a NEFSC protocol section

ACTIVE ACOUSTICS

An active acoustic system (e.g. EK80/echosounder) will be alternated between “ON/ACTIVE” (1200 – 0700) and “OFF/PASSIVE MODE” (0700 – 1200) daily. This is because beaked whales exhibit an acoustic response to echosounders thus we need to balance collecting passive acoustic information on beaked whales, with the need to collect prey layer data from the echosounder, which has been found to be a useful covariate in some species models. The survey technician on board is responsible for changing the echosounder state, however, it is your responsibility to VERIFY that the EK80 has been turned to passive mode based on the proposed schedule. If it has not, find the survey tech and kindly ask them to turn it off.

 If you cannot find the survey tech, contact the bridge and ask for them, if that doesn’t work:

  1. On the Pisces, the EK80 controls are in the acoustics lab toward the galley. To change the status of the echosounder, select “Normal operation” button on the right. Under “Mode” select “Passive” for all echosounder rows. Click “Apply” and “Ok”. This sets the echosounder settings to “OFF”.

  2. Click the sound icon to the right of the “Ping” button to stop transmission.

  3. Remember to turn the echosounder back on at 1130 by doing the inverse steps.

ARRAY CARE

  1. Wash the array and tow cable with a hose (not on high power)

  2. Remove all tape from the connector connecting the array to the tow cable as well as at the tail. Remove the tail

  3. Bring the array to the wet lab and begin array spa

    1. Using a q-tip and alcohol, clean out any salt/water inside the connectors

    2. Can also use canned air

      1. Try not to spray it directly on the o-ring so that it doesn’t become brittle

    3. Look for corrosion and be sure to remove it

    4. Do not bend the pins

    5. Clean the caps as well, removing all salt residue

    6. For a demonstration of this process, please refer to Acoustics_CleaningArray.mov

  4. Once dry, secure it in its pelican case

  5. Be sure to also clean the connectors connecting the tow cable to the deck cable in the same manner

    1. Rinse off any part of the deck cable that was exposed to the elements

  6. Spool the tow cable onto the wooden drum using two jackstands and a pipe

    1. Make sure both connector ends are visible/easy to access

TOWED ARRAY: LOGGER FORMS

  1. Overall NOTES:

    1.  Make sure that Function keys are locked ON

      1. Hold “fn” key and press “Esc” to activate

      2. Important on newer computers

    2. Always fill out Date/Time on each sheet

  2. ARS

    2. Fill out at start of each Leg and then only if something changes in the Leg

    3. Acoustic Recording System

      1. Settings that impact the entire ARS

        1. GPS Unit: Shipboard GPS

        2. Leave rest blank

    4. Recorder 1 (Recording)

      1. Settings for each system

        1. Computer - Recorder computer

        2. Sound Card - NiDAQ

        3. Sampling Rate - 500000 Hz

        4. High pass - 1000 Hz

        5. Fill out each channel and the dB level assigned within PAMGuard module Sound Acquisition (Toolbar: Settings -> Sound Acquisition)

    5. Recorder 2 (Tracking)

      1. Settings for each system

        1. Computer - Tracking

        2. Sound Card - NiDAQ

        3. Sampling Rate - 250000 Hz (There is a decimator in place)

        4. High pass - 2000 Hz

        5. Fill out each channel and the dB level assigned within PAMGuard module Sound Acquisition (Toolbar: Settings -> Sound Acquisition)

    6. Click SAVE

  3. Array

    2. Fill out at start of each leg and then only if something changes in the Leg

      1. Array Weight: 30 lbs

      2. Array Name 1 - Echidna array selected

      3. Separator - 0 m

      4. Array Name 2 – leave blank

      5. Leave rest blank

      6. Click SAVE

  4. Deploy (not used)

  5. Detection (1,2,3)

    2. There can be up to 3 active detections at one time using the forms

      1. If all you are is waiting on an End Time to close the detection and another form is needed, then Save the entry and put the End Time in the Comments Tab (ex: *End Time AC2 06/19/2023 12:12:12)

      2. All acoustic detection distances should be reported in meters

      3. To save the detection there must be a minimum of 3 signals (clicks or whistles) and at a minimum record the initial bearing angle.

        1. If never detected, write a note in the comments field that the encounter was “untraceable”
        1. If minimum is not met make a comment in the log with what was heard and when

      4. To signify a new group: incoming bearings must be at a smaller angle than the current group’s bearings you are tracking & the original group must be behind 90 degrees (this is because there are lots of individuals/subgroups and can be spread out)

        1. Eg: you are tracking a group and they are at 108 degrees +/- 10 degrees. New clicks come in at 20 degrees. These new clicks would belong to a new group
        1. For the following fields, underline= required field

    3. StartTime Date: Start of detection (auto fill using F1, but correct the time to the initial click or whistle detected on the tracking computer) by either clicking on the click in the T-B plot and reading the time off the waveform, or hovering over the end of the bearing line drawn on the map

    4. EndTime Date: Last signal (click or whistle) detected (auto fill using F1, but correct the time to the last click or whistle detected on the tracking computer) using the same methodology as in 5.c.i

    5. Location: Autofill with F1 within 2 minutes of start time

      1. If there has been more than 2 minutes from the StartTime to filling in the field then place this comment in the Detection’s comment box (*Edit Lat/Lon to StartTime). If you’ve made a map comment for the start of the event, you can get that value in data QAQC (*see map comment for position of A1)

    6. Acoustic ID: Start with 1 at beginning of cruise and continue counting until end of the project (do NOT start over each Leg)

    7. Visual ID: Sighting ID number from Visual time that matches current detection

      1. If never seen, leave blank

      1. Initial Angle: First angle detected from either a click or whistle

      2. Initial Distance: Location at start of localization

        1. If never localized then fill in NA for units

      3. Beam Distance: Perpendicular distance from the beam (90 degrees) of the array to the first subgroup of animals

        1. With timestamp

        2. If never localized then fill in NA for units

      4. Detection Distance: Greatest distance animals were detected from the array. That can be the same as Initial or Beam distance.

        1. If never localized then fill in NA for units

      5. Localization Method: If any of the distances were measured then select Pamguard, otherwise NA.

      6. Vocals detected: Select as many vocal types that were present at any point throughout the detection (order does not matter)

      7. Detection Type: Acoustics or Both. Never use Visual as an option for this field. All Visual only sightings can be recorded in the User input.

      8. First Detection: Acoustics, Visual, or Both (Whomever’s start time is earliest). 

      9. Method: Acoustic Technician

      10. Species Code 1: Select species acoustics detects and fill out 2 & 3 if needed.

      11. Additional Method fields are to be filled out if Visuals has a species ID. They don’t have to match acoustics. Example: Visuals has Unid. beaked whale, but Acoustics detects Cuvier’s beaked whales. OR Visuals has sperm whales and Acoustics detects sperm whales & Unid. dolphins.

      12. Comments: Any additional information of note from the detection. If the field is filled then add additional information in the User input. Add the UID number so we can match the PAMGuard annotations to the Acoustic ID later

    8. Click SAVE

  6. Effort

    2. Fill out at every shift change and/or change in effort status

      1. StartTime Date: auto fill using F1

      2. Cruise Number: e.g. PC2501

      3. Trackline ID: Leave empty if off the trackline, fill in the trackline number if on effort and on track

      4. Acousticians: Those present in the chairs. The first one is the person on effort, the second one is for the standby acoustician

      5. Effort

        1. Acoustic: ON when acousticians are monitoring the recordings

        2. Visual: ON when members of the Visual team are on the flying bridge (or bridge) regardless of their effort status. Make a comment if they are on weather watch (PIFSC surveys, for NEFSC the chief sci does this)

        3. Recording: ON when data is being collected

        4. Other effort: echosounder status (ON/OFF)

      6. Real-time Monitoring: Select the channels being monitored on the tracking computer

      7. Sound speed: enter the soundspeed from the most recent bongo

      8. Sea state: if an observer is in the dry lab ask them, otherwise determine it yourself

      9. Leave the rest blank

      1. Click SAVE

  7. Sperm whale (NEFSC only)

    2. Start/End Time

    3. Start/End latitude and longitude

    4. ID (46-Sperm Whale) and ID type (acoustic tech, visual, or both) 

    5. Call type detected (Usual, Coda, etc)

    6. Localization not required, but feel free to practice if clicks registering on detector and nothing else is happening (NEFSC only).  

    7. Comments should contain a rough estimate of how many sperm whales are in the event

  8. Playback (NEFSC only)

    1. Refer to Appendix III link

    For further details, please refer to the >>>>>>> parent of 17286fc (Added Data QAQC, Array care, Logger forms, and active acoustics section from NEFSC manual)