Surveying a kuakua / large dog cockle shell drift

I was stoked to stumble across this kuakua shell drift North West of Waiheke Island. It adds a lot of complexity to the seafloor and is fun to explore because of the biodiversity it hosts. I imagined it was one large drift that I could map by attempting to swim around it at slack tide. To do this I dragged a float on the surface with my son’s phone attached. The phone was using MapMyRun as I am very familiar with the app. A plastic container was screwed to the float to hold the phone which was encased in two plastic bags, the lid of the container was also taped to the float). I had a friend on the surface follow me in a small boat with a Garmin Explorer Plus (this also helped with safety and was essential to help me get back to the boat against the current).

Edge of the kuakua shell drift

The bed is dominated by kuakua but also included large long trough shells (Oxyperas elongatum) and tipa / scallop shells further out. I used these large shells as the edge of the drift rather than the smaller shells. It was tempting to use the high contrast line created by dark red algae growing on undisturbed (but often smaller tawera spissa) shells which contrasted with the white shell hash. I took my phone to record marine life, logged on Many of the sponges were hard to identify as I was not using a dive light and the warm colours are missing.

The time stamps on my photos and the length of the dive on my dive computer were useful but the timestamps on the individual tracking points on the Garmin were essential to identify the dive path. This is because I needed to remove tracking points generated:

  1. Before the dive from boat movement
  2. While I drifted during my safety stop
  3. After the dive while being towed back to my boat

Although I ran out of air before I could get around the whole drift (44minute dive) the tracking data gives a sense for the size of the drift. By joining the start and endpoints the track roughly made a four sided shape for which I could calculate the area (16,813m2 or 0.017km2) by dividing it into two triangles and applying Heron’s Formula.

There were some small gaps in the drift and I’m sure the habitat exits outside the area I tried to circle, I felt like it was more dense in the NW where there was also more tipa shell. I’d like to make a little drop camera to get a better sense for the seafloor habitats surrounding the surveyed area. I would also like to try doing some photogrammetry showing the diversity in the drift , to do this I need to build a cage for my GoPro that I can attach lights to.

Erosion in Wai O Taiki Bay

A 2016 Tonkin & Taylor report on the erosion of the banks of the Tamaki Estuary in Wai O Taki Bay suggested a 3-5 m/100 year range rate of retreat. I took some photos in 2013 so wanted to see if the prediction looked right for the last seven years.

The 2021 photo has more grass and that the failing fence is not keeping people off the closed track.
The 2021 photo has more exposed bedrock showing a loss of soil. The flax bush is now very exposed to elements and will likely die in the next few years. Soil loss is apparent adjacent to the unfinished seawall.
The 2021 photo shows how the harder substrate has changed its shape. Roosts of dead pine rotting and stumps falling down slope. Wilding pine growth.
There is an increased distance between unfinished seawall and clay bank in the 2021 photo. Loss of clay bank. Subsidence affecting stability of trees.
Since 2013 more bedrock has been exposed adding about a tonne of clay sediment to the Estuary. Wilding pines and gorse are the dominant species. An exposed root at the top of the bank indicates 20-50cm retreat.
The 2021 photo shows an increase in mangrove coverage and a reduction in flax.
Note these images are over a different time period. Omaru Island is clearly eroding (source data on GeoMaps).

My best guess would be about 30cm of loss over the seven year period suggesting the prediction to be about right.

The report suggested a ‘Do nothing’ option which was adopted by the Local Board.  The exposed banks are at least 100m long and average about 2m high. If we lost 30cm of bank over the last seven years that’s 60 cubic meters of clay and top soil. Wet excavated clay weighs 1,826 kg/m³, so more than 100 tones of life choking sediment dumped into the Tāmaki Estuary and the Hauraki Gulf (on our watch).

This report has been submitted to the Maungakiekie-Tāmaki Local Board.

Update September 2022. I was invited to present this report to the Local Board a year later. It was well received and has been recorded in their minutes.

What’s at the bottom of Jones Bay Lagoon?

I have driven past Jones Bay Lagoon many times and always wondered what’s down there. It was dredged for shingle from about 1870-1950 and would have had a stony seafloor like Jones Bay. I had heard that the mining might have made the lagoon 20 meters deep. Altho I knew there was sediment around the edges I imagined it was quite stable as most of the receiving catchment has been reforested including the regions best example of a wetland (albeit a small one).

Areas explored in green

I made a few transects at high tide. There was no noticeable current and the visibility above 4m was about 3m. However nearing the 5m mark the visibility dropped to .2m and was not much fun. I was able to easily plunge my hand into the seafloor about 30cm deep before it got uncomfortably sticky and heavy, the mud was very dark grey. The deepest spot I found was 7.5m with most of the lagoon at 5m. The contour of the seafloor varied and did not make sense with the odd ridge appearing in unexpected places.

I saw several fish including, a school of spotty, many yellow-eyed mullet in the shallows, a few snapper, and what I think were estuarine triplefin.

No Fishing. Marine pests found in this lagoon.

The biggest surprise however was the no fishing signs erected by Auckland Council. I was pleased to see them as it has always felt wrong to allow killing of native species in the Regional Park, which is supposed to be a safe place for nature. It was also a surprise given my recent request for Council to start managing the effects of fishing. This sign however is only here to manage a marine pest called Eudistoma or the Australian droplet tunicate.

Eudistoma are the little white things, the stalks belong to Mediterranean fanworm.

I knew that Eudistoma had reached the park because I was alerted by a member of the public on the 4th of February. It was no surprise as they were spreading fast and I documented dense areas of them on the other side of Kawau Bay in February 2019. The lagoon also had large numbers of Mediterranean fanworm (another marine pest) which interestingly often hosted native pleated sea squirts which I have not noticed on fanworm elsewhere. Mediterranean fanworm and Eudistoma are both present in the ocean, meters from the mouth of the lagoon. There was one small cockle bed in a sandy area and several areas with pacific oysters in the shallows. I have asked Auckland Council to comment on the closure which happened in spring 2020.

The Coastal Marine Area boundary on Unitary Plan viewer

Response from Auckland Council below.

The coastal marine boundary follows the South Coast/Jones Bay foreshore of Tāwharanui Regional Park, thus the lagoon is within the regional park, or at very least the land around it.

Fishing here is inconsistent with the general Regional Parks Management Plan to not take flora and fauna. The unwanted organism would be a threat to the Tāwharanui Marine Reserve. The regional parkland provides land based access to the periphery of the reserve and there is a real risk of transfer of organism in viable state on wet fishing gear between the two sites. The identification of the tunicate prompted a management response.

A short photogrammetric transect (4-5m)
Another slightly longer one, the fanworm are not as clear as I had hoped, I need to get much better at over-laping the frames.

I am making sure to decontaminate my dive gear, and I do not recommend the area for diving, in fact I think it might be with looking at the sediment inputs and, if they are low, considering the site for mussel bed restoration.

Birds of Auckland

Birds of Auckland

In 1980 the New Zealand Herald published a book called “Birds of Auckland” by Tim Lovegrove. It’s a great little book with great photos and detailed illustrations. I was only 5 years old in 1980 and lived in Whangārei so I found it interesting to read how these places have changed. However there are better datasets for a more robust analysis of population trends. I made some notes while I read it:

P7. “Tahuna Torea nature reserve at Glendowie is easily accessible from the city. Here many shorebirds gather to roost at high tide or feed on the nearby mud-flats at low water.” This site is also mentioned on page 57.

We know from other data that this roost has been compromised and species like godwit and knots no longer using the roost.

P15. “Giant petrels or nellies are common winter visitors to the Hauraki Gulf. These large, dark birds venture well into the Waitemata Harbour, often following ships. One can often see them from Tamaki Drive or Oarkie Wharf, if ships coming and going from the port are watched carefully with binoculars. Nellies follow in the wake of ships ready to scavenge upon any galley scraps tossed overboard.”

It’s good we no longer see giant petrel following ships, I expect this is because humans are now less likely to throw their waste overboard.

P33. [Pied shag] “Breeding colonies are located in the suburbs at the Panmure and Orakei Basins, and on the edges of Lake Pupuke.”

The colony at Panmure is probably 1/30th the size it was. I believe the Lake Pupuke colony has moved to the Chelsea Sugar factory but I am not sure.

P37. [Little shag] “There is a well-established colony in Hobson Bay where some 30 pairs of little shags breed.”

This colony is gone, tho I note a similar size colony has started at Point England in late 2019.

P39. “A number of spotted shags may be seen at high-tide roost on the rocks beside the Kawakawa Bay to Kailua road at Tarata Point. Another colony may be seen at Ihumoana Cliff at Bethells.”

We no longer see spotted shags at these locations or near the mainland.

P39. [White heron] “A regular visitor to the northern harbours of Manukau, Kaipara and Firth of Thames during winter.”

Observations of kotuku are now quite rare with less than 50 ever being recorded on

P45. [Royal spoonbill] “… an occasional winter visitor to harbours and estuaries in the Auckland district”

Observations of Spoonbills are way up with more than 1,200 records on

P45. [Canada goose] “… appears only as a straggler in the Auckland district.”

Observations of Canada geese are way up with more than 1,200 records on

P52. [Weka] “… are also established around Middlemore Golf Course following a release of 18 birds at Kings College in 1971”

They didn’t survive but its interesting to hear about these early efforts.

P60. [Variable oystercatcher] “These days beach buggies pose the greatest threat to their breeding grounds. Only the odd variable is ever seen among the vast flocks of South Island pied oystercatchers in the Manukau, Kaipara and Firth of Thames.”

Beach buggies are no longer a significant threat. Observations of VOC are definitely up and the species is recovering.

P60. “Small flocks of up to 100 golden plover may occur in the South Manukau and Firth of Thames”.

Golden plover numbers have declined sharply.

P63. [Banded dotterel] Here over 100 birds are regularly found during the winter on the short cropped pasture of the freezing works holding paddocks on Hamlins Hill.

No waders are ever seen on Hamlin’s Hill anymore which has just been made a Regional Park.

P63. [New Zealand dotterel]. “It is a breeding bird near Auckland in the South Manukau and Firth of Thames.”

The strongest breeding grounds are now north east of Auckland from Shakespear Regional Park to Mangawhai.

P77. “Native pigeons still occur in reasonable numbers in the Waitakere and Hunua Ranges. Odd birds appear in the suburbs every year, especially in parks and gardens with fruiting trees”

This description sounds very sparse. They are rarely seen in eastern suburbs but are quite resident in many other suburbs. I’m sure Aucklands kereru numbers have risen strongly with predator control.

P78. [Kaka] “… are present in small numbers in the Waitakere and Hunua Ranges. These large parrots seem to be occasional winter visitors to suburban Auckland, as every year there are reports of birds from places like Cornwall Park and the Domain.”

It sounds like Kaka numbers have dropped in the Waitakere and Hunua Ranges and suburban Auckland, I would say that the Gulf Islands and Mainland Sanctuaries are now the best places to find Kaka.

From a handbook perspective, Aucklands avian populations have changed a lot with some significant improvements for many species which is impressive given Aucklands human population more than doubled in the last 41 years.

Kelp gardening

Community groups and scientists have begun ‘Kelp Gardening’ in the Hauraki Gulf. The activity involves removing kina (se urchins) from rocky reefs to allow the kelp to regrow. It gives divers and snorkelers something to do on a reef (where they no longer have fish to hunt) and fits nicely with New Zealand pest management ethos (suppression).

However kina are not a pest, their numbers are artificially inflated by overfishing. See diagram of mine from the State of the Gulf report below.

Kina barrens are created by overfishing

Kelp gardening differs wildly from other active restoration techniques as it replaces a natural function with a human intervention. The activity may have a place in the creation of a marine protected area but it is not a smart long term reef management technique because it treats the symptom not the cause of a sick reef.

So why are well respected scientists and well intentioned volunteers doing it? I really think it’s just because calls for marine protection have fallen on deaf ears, and some people are so desperate to fix things they will try anything.

UPDATE: 11 March 2021: In a public seminar today Dr Nick Shears who is an expert on kina barrens in New Zealand said “kina removal can be incorporated into restoration / management but we want to make it clear it is not the answer on its own!

North Island Snipe

North Island Snipe

I was inspired to make this illustration of the now extinct North Island Snipe by this short paper of Mike Lee’s questioning their prehistoric mainland extinction. I have just finished reading his book Navigators and Naturalists: French Exploration of New Zealand and the South Seas (1769-1824) where he tells the stories of the first French explorers to New Zealand. In 1820 Captain Richard Cruise recorded shooting a snipe on Motukorea (Browns Island) where I monitor shorebirds now.

Māori introduced the Pacific rat kiore, which is thought to be the main driver in the extinction of the North Island Snipe. I have never seen a kiore (that I know of). It was interesting to read how the small rats were an important food source for Māori and that some coveted the larger rats bought by the Europeans.

The illustration was difficult because the only specimen of the North Island snipe has deteriorated. Colin Miskelly provided invaluable advice and corrections, I learnt a lot in the process. I’m very proud to have the image published on New Zealand Birds Online.

A moat for dotterel

I am working with the Auckland Council mowing team to manage the grass for Northern New Zealand dotterel which are a conservation dependant species. In the Tāmaki Estaury there are no significant beaches, so the dotterel nest in the grass at Point England.

We need to mow the grass so that:

  • Dotterel can walk in it
  • Dotterel can see predators coming
  • We don’t provide food for predators (rats and pukeko)

However we can’t mow near the chicks and the chicks also need cover from predators. I did ask the grass to stop growing at 10cm but it did not listen to me 😀

We currently have at least two chicks who are always seen with 2-6 adults near the old nest. I considered multiple mowing strategies and decided to trial a moat around the edge of the paddock to exclude agoraphobic predators (rats and cats).

So far the chicks are staying in the un-mown area, adults come and go but generally prefer the mown areas for roosting. I have used a line trimmer to create a shorter grass area in the centre which the adults keep their chicks near.

< 48hr old chick with egg tooth visible

UPDATE: 2 December

I was surprised to find a new three egg nest inside mown moat. Unfortunately it was abandoned on the 11th of December. All three chicks did not fledge and were not seen outside the un-mown area. They looked to prefer the areas where the buckhorn plantain seed heads were less abundant and there was more buttercup.

Mapping life on the seafloor

I’m experimenting with mapping the seafloor for restoration projects. This is what I have done so far:

  1. Record a time-lapse sequence, swim as slow as possible (GoPro Hero 7 Black linear 0.5sec)
  2. Buy ArgiSoft Metashape Standard (about $300NZD)
  3. Import photos to chunk
  4. Align photos (Duplication errors on highest, high best, Reference preselection [sequential], Guided image matching)
  5. Don’t clean up the point cloud (not needed for orthomosaics)
  6. Build mesh (use sparse cloud source data, Arbitrary 3D)
  7. Build texture (Adaptive orthophoto, Mosaic, Enable hole filling, Enable ghosting filter)
  8. Capture view (hide cameras and other visual aids first then export .PNG at a ridiculous resolution)

ArgiSoft Metashape worked much better than using Adobes photo stitching software (Photoshop & Lightroom) on the same data. But I need more overlapping images as all the software packages were not able to match all of any of the four test sequences I did.

I’m going to test shooting in video next. The frames will be smaller 2704×1520 (if I stick with linear to avoid extra processing for lens distortion) instead of 4000×3000 with the time-lapse but I’m hopping all the extra frames will more than compensate (2FPS=>24FPS).

In theory an ROV will be better but I don’t think there are any on the market that know where they are based on what they can see. All the work arounds for knowing where you are underwater are expensive, here are two UWIS & Nimrod. I want to see if we can do this with divers and no location data. I don’t think towing a GPS will be accurate enough to match up the photos but it does seem to work with drones taking images of bigger scenes (I want this to work in 50cm visibility). I expect if I want large complete images the diver will need to follow another diver who has left a line on the seafloor. One advantage of this is that the line could have a scale on it, but I’m hoping to avoid it as the lines will be ugly 😀 So far I can do only two turns before it fails. There are three patterns that might work (Space invaders, Spirals and Pick up sticks). For my initial trials I am focusing on Space invaders.

Video provides lots more frames and the conversion is easy. A land based test with GPS disabled, multiple turns, 2500 photos, 2704 x 2028 linear, space invader pattern at 1.2m from the ground worked perfectly. However I cant get it to work underwater. In every test so far Metashape will only align 50-100 frames. I tried shooting on a sunny day which was terrible as the reflection of the waves dancing on the seafloor confuses the software. But two follow up shoots also failed, when I look at the frames Metashape cant match I just don’t see why its can’t align them. Theses two images are in sequence, one gets aligned and the next one is dropped!

Here is what the test footage looks like, I have increased the contrast.

I have also tried exporting the frames at 8fps to see if the alignment errors are happening because the images are too similar but got similar results (faster).

Detailed advice from Metashape:

Since you are using Sequential pre-selection, you wouldn’t get matching points for the images from the different lines of “space invader” or “pick up sticks” scenarios or from different radius of “spiral” scenario.

If you are using “space invader” scenario and have hundreds or thousands of images, it may be reasonable to align the data in two iterations: with sequential preselection and then with estimated preselection, providing that most of the cameras are properly aligned.

As for the mesh reconstruction – using Sparse Cloud source would give you very rough model, so you may consider building the model from the depth maps with medium/high quality in Arbitrary mode. As for the texture reconstruction, I can suggest to generate it in Generic mode and then in the model view switch the view from Perspective to Orthographic, then orient the viewpoint in the desired way and use Capture View option get a kind of planar orthomosaic projection for your model.

Align ‘sequential’ only ever gets about 5% of the shots. Repeating the alignment procedure on ‘estimated’ picks up the rest but the camera alignment gets curved. I think I have calibrated the cameras to 24mm (it’s hard to see if that has been applied) but it doesn’t seem to change things.

I tried an above water test and made a two minute video of the Māori fish dams at Tahuna Torea. I used the same settings as above, but dropped the quality down to medium. It looks great!

The differences between above and below water are: Camera distance to subject, flotsam, visibility / image quality and colour range. If the footage I am gathering is too poor for Metashape to align it might mean we need less suspended sediment in the water to make the images. That’s a problem as the places I want to map are suffering from suspended sediment – which is why they would benefit from shellfish restoration.

The Agisoft support team are awesome. They processed my footage with f = 1906 in the camera calibration, align photos without using preselection and a 10,00 tie point limit. The alignment took 2.5 days but worked perfectly (click on the image below). There are a few glitches but I think the result is good enough for mapping life on the seafloor. I will refine the numbers a bit and post them in a seperate blog post, wahoo!

Update Jul 2022: Great paper explaining the process with more sophisticated hardware

Final method

Here is my photogrammetry process / settings for GoPro underwater. I am updating them as I learn more. Please let me know if you discover an improvement. Thanks to Vanessa Maitland for her help refining the process.

Here is an example image made using the process, the area is about 8m in diameter, click on the image to see it full size.

Step 1: Make a video of the seafloor using a GoPro

  • If you’re at less than 5m deep you will need to go on a cloudy day for even light
  • Make sure you shoot 4k, Linear. Also make sure the orientation is locked in preferences.
  • Record you location and the direction your going to swim if you want to put your orthomosaic on a map
  • Swim in a spiral using a line attached to a peg to keep the distance from it even
  • Don’t leave any gaps or you will generate a spherical image

Step 2: Edit your video

  • There are lots of software packages that will do this, I use Adobe After FX where I can increase the contrast in the footage and add more red light depending on the depth. You might also find it easier to trim your video here but you can also do it in Step 5.

Step 3: Install and launch Agisoft Metashape Standard.

  • These instructions are for version 1.8.1

Step 4: Use GPU.

  • In ‘Preferences’, ‘GPU’ select your GPU if you have one, I also checked ‘Use CPU when performing accelerated processing’

Step 5: Import video

  • From the menu chose: ‘File’, ‘Import’, ‘Import Video’.
  • The main setting to play with here is the ‘Frame Step’ We have had success with using every third frame which cuts down on processing time.
  • If you have multiple videos you will have to import multiple chunks, then I recommend combining them before processing using ‘Workflow, Merge Chunks’, I have had better results doing this, rather than processing each chunk individually then choosing ‘Workflow, Align Chunks’.

Step 6: Camera calibration

  • From the menu chose: ‘Tools’, ‘Camera calibration’
  • Change ‘Type’ from ‘Auto’ to ‘Precalibrated’
  • Change the ‘f’ value to 1906

Step 7: Align photos

  • From the menu chose: ‘Workflow’, ‘Align Photos’
  • Check ‘Generic preselection’
  • Uncheck ‘Reference preselection’
  • Uncheck ‘Reset current alignment’
  • Select ‘High’ & ‘Estimated’ from the dropdown boxes
    Under ‘Advanced’ chose:
  • ‘Key point limit’ value to 40,000
  • ‘Tie point limit’ value to 10,000
  • Uncheck ‘Guided image matching’ & ‘Adaptive camera model fitting’
  • Leave ‘Exclude stationary tie points’ checked

If 100% of cameras are not aligned then try Step 8 otherwise skip to Step 9.

Step 8: Align photos (again)

  • From the menu chose: ‘Workflow’, ‘Align Photos’
  • Uncheck ‘Generic preselection’
  • Check ‘Reference preselection’
  • Uncheck ‘Reset current alignment’
  • Select ‘High’ & ‘Sequential’ from the dropdown boxes
    Under ‘Advanced’ chose:
  • ‘Key point limit’ value to 40,000
  • ‘Tie point limit’ value to 4,000
  • Uncheck ‘Guided image matching’ & ‘Adaptive camera model fitting’
  • Leave ‘Exclude stationary tie points’ checked

Now all the photos should be aligned, if not repeat step 7 & 8 with higher settings and check ‘Reset current alignment’ on step 7 only. I have been happy with models that have 10% of photos not aligned.

Step 9: Tools / Optimize Camera Locations

Just check the check boxes below (default settings):

  • Fit f, Fit k1, Fit k2, Fit k3
  • Fit cx, cy, Fit p1, Fit p2

 Leave the other checkboxes (including Advanced settings) unchecked.

Step 10: Resize region
Use the region editing tools in the graphical menu make sure that the region covers all the photos you want to turn into a 3D mesh. You can change what is being displayed in the viewport under ‘Model’, ‘Show/Hide Items’.

Step 11: Build dense cloud

  • Quality ‘High’
  • Depth filtering ‘Moderate’
  • Uncheck all other boxes.

Step 12: Build mesh

  • From the menu choose: ‘Workflow’, ‘Build Mesh’
  • Select ‘Dense cloud’, ‘Arbitrary’
  • Select ‘Face count’ ‘High’
  • Under ‘Advanced’ leave ‘Interpolation’ ‘Enabled’
  • Leave ‘Calculate vertex colours’ checked

Step 13: Build texture

  • From the menu choose: ‘Workflow’, ‘Build Texture’
  • Select ‘Diffuse map’, ‘Images’, ‘Generic, ‘Mosaic (default)’ from the dropdown menus.
  • The texture size should be edited to suit your output requirements. The default is ‘4096 x 1’
  • Under ‘Advanced’ Turn off ‘Enable hole filling’ & ‘Enable ghosting filter’ if you’re using the image for scientific rather than advocacy reasons.

Step 14: Export orthomosaic
You can orientate the view using the tools in the graphical menu. Make sure the view is in orthographic before you export the image (5 on the keypad). Then chose ‘View’, ‘Capture View’ from the menu. The maximum pixel dimensions are 16,384 x 16,384. Alternatively you can export the texture.


Let me know if you have experimented converting timelaspe / hyperlapse video to photogrammetry. There may be some advantages.

Stream Health Monitoring guides

As communities get increasingly worried about the declining quality of their waterways there is more interest stream health assessments. I am a huge fan of the Waicare Invertebrate Monitoring Protocol (WIMP) which is simple enough that school students can use it. However the Waicare programme has been largely defunded by Auckland Council and there is no way for the public to share WIMP data. NIWA and Federated Farmers of New Zealand have put together based on the New Zealand Stream Health Monitoring and Assessment Kit (SHMAK). It is great but incredibly hard to use, the manual is horrific. I believe this is being addressed but will take years. To help, the science learning hub has made this great guide for teachers and students. NIWA have put together some videos. They are not published together anywhere online so I have posted the list below: