title: Occlusion prediction for kiwifruit yield estimation

authors: Seabright, Matthew James

subjects: kiwifruit

abstract: Kiwifruit is very important to the New Zealand economy, bringing in NZ$2.39 billion in the 2017/2018 season and projected to grow to NZ$4.5 billion by 2025. Every season, the expected yield from each orchard is estimated. These estimates are used for both on-orchard decisions regarding thinning and spraying, and industry level decisions regarding export pricing, supply agreements, labour requirements, packaging quantities and more. The current method for yield estimation is manual and prone to errors. In the 2016/17 growing season, green kiwifruit estimates were 5.9% lower than actual harvest yield, resulting in over 5 million trays (approximately 18,000 tons) of fruit being disposed of.

An automated system could reduce errors saving the industry significant amounts of money. Such a system could realise other benefits such as providing more granular information on orchard performance to growers and increasing labour efficiency and crop uniformity via targeted labour. Other automated fruit yield estimation systems have been developed but have suffered from sub-optimal performance due to occlusion of fruit. The work presented here introduces a system that has been developed with the aim of minimising occlusion where possible and employs an occlusion prediction model to account for remaining occlusion. The system utilises stereo vision, a 3D lidar unit, an inertial measurement unit and LED lighting mounted on an all terrain vehicle (ATV).
Data is captured across 16 maturity areas, consisting of 33.9 Ha of commercial kiwifruit orchards. A simultaneous localisation and mapping system is used to locate the ATV within the orchard. A convolutional neural network detects kiwifruit, which are localised via stereo triangulation. Individual fruit are tracked through overlapping images to reduce occlusion while ensuring no double counting. Fruit are counted and an occlusion prediction model is applied to account for the unseen fruit.

The system is able to predict orchard scale fruit yield with a mean absolute percentage error of 0.68%. This error rate was obtained from an independent test dataset and ground truth data obtained from a commercial kiwifruit packhouse. The system can also generate visualisations of orchards showing all individual detected fruit in 3D, fruit density maps and canopy density maps. The ability of the system to predict yield with high accuracy and at orchard scale sets it apart from previous work. It is also the largest scale study currently known, consisting of over 15 million fruit.

text: Occlusion prediction for kiwifruit yield estimation Kiwifruit is very important to the New Zealand economy, bringing in NZ$2.39 billion in the 2017/2018 season and projected to grow to NZ$4.5 billion by 2025. Every season, the expected yield from each orchard is estimated. These estimates are used for both on-orchard decisions regarding thinning and spraying, and industry level decisions regarding export pricing, supply agreements, labour requirements, packaging quantities and more. The current method for yield estimation is manual and prone to errors. In the 2016/17 growing season, green kiwifruit estimates were 5.9% lower than actual harvest yield, resulting in over 5 million trays (approximately 18,000 tons) of fruit being disposed of.

An automated system could reduce errors saving the industry significant amounts of money. Such a system could realise other benefits such as providing more granular information on orchard performance to growers and increasing labour efficiency and crop uniformity via targeted labour. Other automated fruit yield estimation systems have been developed but have suffered from sub-optimal performance due to occlusion of fruit. The work presented here introduces a system that has been developed with the aim of minimising occlusion where possible and employs an occlusion prediction model to account for remaining occlusion. The system utilises stereo vision, a 3D lidar unit, an inertial measurement unit and LED lighting mounted on an all terrain vehicle (ATV).
Data is captured across 16 maturity areas, consisting of 33.9 Ha of commercial kiwifruit orchards. A simultaneous localisation and mapping system is used to locate the ATV within the orchard. A convolutional neural network detects kiwifruit, which are localised via stereo triangulation. Individual fruit are tracked through overlapping images to reduce occlusion while ensuring no double counting. Fruit are counted and an occlusion prediction model is applied to account for the unseen fruit.

The system is able to predict orchard scale fruit yield with a mean absolute percentage error of 0.68%. This error rate was obtained from an independent test dataset and ground truth data obtained from a commercial kiwifruit packhouse. The system can also generate visualisations of orchards showing all individual detected fruit in 3D, fruit density maps and canopy density maps. The ability of the system to predict yield with high accuracy and at orchard scale sets it apart from previous work. It is also the largest scale study currently known, consisting of over 15 million fruit.

year: 2020

title: Does seagrass influence the behavioural and physiological response to flow in juvenile snapper (Pagrus auratus)?

authors: Cooper, Jordan

subjects: Seagrass habitats

abstract: Many juvenile fish species are associated with structural habitats, potentially benefiting them from reduced predation and competition as well as enhanced feeding opportunities. It is also possible that structural habitats may provide a refuge from flow. Research on juvenile snapper in New Zealand has largely focused on their habitat preference. Juvenile snapper (Pagrus auratus) have been observed in close proximity to seagrass (Zostera muelleri) in New Zealand estuaries and I tested whether this association offered a refuge from flow. In an annular flume I exposed two cohorts of juvenile snapper 4.1 ± 0.5 cm and 8.9 ± 0.7 cm in length to sequential increases of flow speed (approximately 1 body length per second every 15 minutes). Flow speed increased at 3 cm s⁻¹ every 15 minutes for the smaller cohort of juvenile snapper, and 8 cm s⁻¹ for the larger cohort of juvenile snapper. Juvenile snapper were exposed to three treatments comprising of; bare, mixed (seagrass, bare and edge habitat) and full seagrass coverage. Fish behaviour was observed and critical swimming speed (Ucrit) estimated (i.e. the flow at which fish can no longer maintain position). Juvenile snapper were exposed to flow speeds that are representative of current flows in New Zealand estuaries and harbours. A startle response was recorded at the end as an indicator of fatigue and from larger juveniles a blood sample was collected via caudal puncture to determine if there were any physiological advantages offered by seagrass, by analysing stress indicators (based on lactate, triglyceride, glucose, haemoglobin and haematocrit).

Velocity profiles indicated that the seagrass treatment and sampling points 2 (seagrass upstream and downstream) and 9 (5 cm into the leading edge of seagrass) from the mixed treatment dampened the flow speed within the annular flume. This result may be responsible for the increased percentage of time spent utilising the edge habitat as flow velocity increased, indicating that juvenile snapper seek refuge from high flows in or on the leading edge of seagrass patches. These results are consistent with an increase in critical swimming speed with increasing seagrass coverage (smaller juvenile snapper – bare = 19.47, mixed = 21.13, seagrass = 21.66 cm s⁻¹) (larger juvenile snapper – bare = 52.23, mixed = 58.89, seagrass = 60.31 cm s⁻¹). Physiological indicators, triglyceride, yielded significant differences between the bare treatment (1.40 mM) compared to the mixed (1.05 mM) and seagrass (1.01 mM) treatments, suggesting that energy stores were more readily utilised as energy expenditure increased where structural complexity was absent. The bare treatment also produced the highest values for both lactate and glucose, however, results were not significant. Mean cell haemoglobin concentration and total haemoglobin concentration did not yield significant differences between treatments. Whilst producing positive trends, results suggest that the effect of structural complexity was subtle in the annular flume. These findings have important implications for other hypotheses to explain the association between juvenile snapper and seagrass beds.

text: Does seagrass influence the behavioural and physiological response to flow in juvenile snapper (Pagrus auratus)? Many juvenile fish species are associated with structural habitats, potentially benefiting them from reduced predation and competition as well as enhanced feeding opportunities. It is also possible that structural habitats may provide a refuge from flow. Research on juvenile snapper in New Zealand has largely focused on their habitat preference. Juvenile snapper (Pagrus auratus) have been observed in close proximity to seagrass (Zostera muelleri) in New Zealand estuaries and I tested whether this association offered a refuge from flow. In an annular flume I exposed two cohorts of juvenile snapper 4.1 ± 0.5 cm and 8.9 ± 0.7 cm in length to sequential increases of flow speed (approximately 1 body length per second every 15 minutes). Flow speed increased at 3 cm s⁻¹ every 15 minutes for the smaller cohort of juvenile snapper, and 8 cm s⁻¹ for the larger cohort of juvenile snapper. Juvenile snapper were exposed to three treatments comprising of; bare, mixed (seagrass, bare and edge habitat) and full seagrass coverage. Fish behaviour was observed and critical swimming speed (Ucrit) estimated (i.e. the flow at which fish can no longer maintain position). Juvenile snapper were exposed to flow speeds that are representative of current flows in New Zealand estuaries and harbours. A startle response was recorded at the end as an indicator of fatigue and from larger juveniles a blood sample was collected via caudal puncture to determine if there were any physiological advantages offered by seagrass, by analysing stress indicators (based on lactate, triglyceride, glucose, haemoglobin and haematocrit).

Velocity profiles indicated that the seagrass treatment and sampling points 2 (seagrass upstream and downstream) and 9 (5 cm into the leading edge of seagrass) from the mixed treatment dampened the flow speed within the annular flume. This result may be responsible for the increased percentage of time spent utilising the edge habitat as flow velocity increased, indicating that juvenile snapper seek refuge from high flows in or on the leading edge of seagrass patches. These results are consistent with an increase in critical swimming speed with increasing seagrass coverage (smaller juvenile snapper – bare = 19.47, mixed = 21.13, seagrass = 21.66 cm s⁻¹) (larger juvenile snapper – bare = 52.23, mixed = 58.89, seagrass = 60.31 cm s⁻¹). Physiological indicators, triglyceride, yielded significant differences between the bare treatment (1.40 mM) compared to the mixed (1.05 mM) and seagrass (1.01 mM) treatments, suggesting that energy stores were more readily utilised as energy expenditure increased where structural complexity was absent. The bare treatment also produced the highest values for both lactate and glucose, however, results were not significant. Mean cell haemoglobin concentration and total haemoglobin concentration did not yield significant differences between treatments. Whilst producing positive trends, results suggest that the effect of structural complexity was subtle in the annular flume. These findings have important implications for other hypotheses to explain the association between juvenile snapper and seagrass beds.

year: 2015

title: Kōura (Paranephrops planifrons) populations in the Te Arawa lakes: An ecological assessment using the traditional Māori tau kōura harvesting method and recommendations for sustainable management

authors: Kusabs, Ian Andrew

subjects: Kōura

abstract: Freshwater crayfish are amongst the most influential of biota in many aquatic systems. They have various ecological functions, acting as shredders, detritivores and predators which in turn influence other macroinvertebrate fauna. Furthermore, freshwater crayfish are increasingly used as indicator species because of the important role they play in aquatic ecosystems and their iconic and heritage values. Kōura or freshwater crayfish (Paranephrops planifrons White) are endemic to New Zealand where they are an important component of freshwater ecosystems and a source of food for freshwater fish and humans. This study was undertaken to gain a better understanding of kōura populations in the Te Arawa lakes by quantifying relative kōura abundance and distribution and assessing the effects of environmental factors on kōura populations. In addition, basic biological information on sex ratios, breeding and moulting was collected as a basis for setting regulations and management policies for the sustainable management of kōura in the Te Arawa lakes.
Historically, kōura were an important food for the indigenous Māori people, particularly in the central North Island (CNI) lakes where large numbers were harvested for consumption and trading. Today, kōura are considered a ‘taonga’ species and support important customary fisheries in some CNI lakes (Rotomā, Rotoiti, Tarawera, and Taupō) where large populations of kōura still exist. Nevertheless, there is considerable anecdotal evidence of declines in populations of kōura in the Te Arawa lakes district since European settlement. A number of environmental factors have been implicated in this decline, including introductions of exotic fish and plant species as well as reduced concentrations of dissolved oxygen in the bottom waters of lakes due to eutrophication.
Although the ecology of stream-dwelling P. planifrons is well studied in New Zealand, there is limited published biological information on kōura in lakes. The lack of quantitative information on kōura abundance and ecology makes it difficult for iwi (Māori tribes) and government agencies to manage lake dwelling kōura populations. Until recently the main reason for the lack of quantitative information on lake kōura was the absence of suitable representative sampling methods. In a preliminary study of kōura sampling methods in the Te Arawa lakes, it was found that conventional sampling methods, baited traps, SCUBA and underwater video camera surveys had a number of disadvantages. Trapping was found to be highly biased towards large individuals and complicated by reductions in bait quality with time and changes in natural food abundance. SCUBA and underwater video camera surveys are also biased towards large individuals and are strongly dependent on underwater visibility. Given the disadvantages of these conventional kōura assessment methods, a traditional Māori harvesting method, the tau kōura, was adapted for the monitoring of lake kōura populations. The tau kōura captured large numbers and a wide size range (6 – 50 mm Orbit Carapace Length, OCL) of kōura in both shallow (5 m mean depth) and moderately deep water (10 – 17 m depth) in Ōkere Arm and Te Ākau, Lake Rotoiti, respectively. This method also distinguished differences in size structure and biomass between sites and provided information on sex ratios, egg-bearing and moulting. The development of the tau kōura thus enabled research and monitoring of lake kōura populations that may have not previously been representatively sampled and have generally been little studied in New Zealand despite their ecological and cultural significance.
The tau kōura was used to examine population dynamics of kōura, along a eutrophication gradient in seven Te Arawa lakes, in April, July and November 2009. Mean catch per unit effort (CPUE) and depth distribution of kōura were influenced by the combined effects of lake bed sediments, lake morphology, and hypolimnetic conditions related to trophic state. Although limited by the number of lakes that I was able to characterise, my data indicates that lake bed substrate (median sediment particle size) had a stronger influence on population characteristics than the level of enrichment/primary production as indexed by chlorophyll a (Chl-a). Nevertheless, the negative correlations between kōura abundance, with sediment carbon to nitrogen ratio (C/N), and the positive correlation between abundance and Chl-a, suggest that lake productivity does influence kōura. This component of the study indicates that eutrophication has reduced available kōura habitat in the Te Arawa lakes, particularly those that are sheltered, steep-sided and have fine lake bed sediments (with the Rotomahana mud tephra being particularly important). Lake bed substrate composition represented by sediment particle size is therefore a key factor to consider when selecting tau kōura sites for research, monitoring, restoration and harvesting, and when estimating kōura stocks in lakes. I concluded that measures to improve water quality in the Te Arawa lakes should benefit kōura populations by increasing the amount of oxygenated habitat available in the summer and autumn. 
Kōura support important customary fisheries for iwi in some Te Arawa lakes, particularly Rotoiti, Rotomā and Tarawera. However, until recently, there was limited published biological information to provide a basis for fisheries regulations. This knowledge gap has resulted in the adoption of conservative fisheries regulations and management policies by the fishery managers, the Te Arawa Lakes Trust (TALT) and Ministry of Primary Industries (MPI). A further objective of the research was therefore to examine the biological traits of lake kōura and to consider implications of these traits on the current fishing regulations and sustainable management of kōura populations in the Te Arawa lakes. 
From a review of past literature and the research findings from this study, it can be concluded that kōura populations in the Te Arawa lakes are currently not over-exploited due mostly to a low number participating in harvesting (almost exclusively Te Arawa) and because commercial harvesting is prohibited. However, the TALT wishes to encourage the revitalisation of traditional fishing practices (e.g., tau kōura) while adhering to the principles of kaitiakitanga ‒ the sustainable protection of resources. The establishment of sustainable management policies and regulations adheres to the principles of kaitiakitanga.
A number of management changes arising from the information collected in this study are suggested to protect and enhance the kōura fishery in the future. These are (1) set a slot limit with minimum size limit of 28 mm OCL and a maximum size limit of 39 mm OCL, (2) prohibit the taking of egg-bearing females, (3) limit deep-water harvest methods to the use of the tau kōura, and (4) implementing a tau kōura harvest season beginning on 1 December and ending on 31 March. These measures will protect breeding females if they are captured and the closed season will allow the majority of females to breed and release their young prior to fishing activity. Improving water quality (and thus increasing available kōura habitat) and preventing the introduction of predatory fish species such as eels (Anguilla spp.), catfish (Ameiurus nebulosus), and perch (Perca fluviatilis), that are efficient predators of kōura, are of the utmost importance in ensuring the sustainability of kōura populations in the Te Arawa lakes.

text: Kōura (Paranephrops planifrons) populations in the Te Arawa lakes: An ecological assessment using the traditional Māori tau kōura harvesting method and recommendations for sustainable management Freshwater crayfish are amongst the most influential of biota in many aquatic systems. They have various ecological functions, acting as shredders, detritivores and predators which in turn influence other macroinvertebrate fauna. Furthermore, freshwater crayfish are increasingly used as indicator species because of the important role they play in aquatic ecosystems and their iconic and heritage values. Kōura or freshwater crayfish (Paranephrops planifrons White) are endemic to New Zealand where they are an important component of freshwater ecosystems and a source of food for freshwater fish and humans. This study was undertaken to gain a better understanding of kōura populations in the Te Arawa lakes by quantifying relative kōura abundance and distribution and assessing the effects of environmental factors on kōura populations. In addition, basic biological information on sex ratios, breeding and moulting was collected as a basis for setting regulations and management policies for the sustainable management of kōura in the Te Arawa lakes.
Historically, kōura were an important food for the indigenous Māori people, particularly in the central North Island (CNI) lakes where large numbers were harvested for consumption and trading. Today, kōura are considered a ‘taonga’ species and support important customary fisheries in some CNI lakes (Rotomā, Rotoiti, Tarawera, and Taupō) where large populations of kōura still exist. Nevertheless, there is considerable anecdotal evidence of declines in populations of kōura in the Te Arawa lakes district since European settlement. A number of environmental factors have been implicated in this decline, including introductions of exotic fish and plant species as well as reduced concentrations of dissolved oxygen in the bottom waters of lakes due to eutrophication.
Although the ecology of stream-dwelling P. planifrons is well studied in New Zealand, there is limited published biological information on kōura in lakes. The lack of quantitative information on kōura abundance and ecology makes it difficult for iwi (Māori tribes) and government agencies to manage lake dwelling kōura populations. Until recently the main reason for the lack of quantitative information on lake kōura was the absence of suitable representative sampling methods. In a preliminary study of kōura sampling methods in the Te Arawa lakes, it was found that conventional sampling methods, baited traps, SCUBA and underwater video camera surveys had a number of disadvantages. Trapping was found to be highly biased towards large individuals and complicated by reductions in bait quality with time and changes in natural food abundance. SCUBA and underwater video camera surveys are also biased towards large individuals and are strongly dependent on underwater visibility. Given the disadvantages of these conventional kōura assessment methods, a traditional Māori harvesting method, the tau kōura, was adapted for the monitoring of lake kōura populations. The tau kōura captured large numbers and a wide size range (6 – 50 mm Orbit Carapace Length, OCL) of kōura in both shallow (5 m mean depth) and moderately deep water (10 – 17 m depth) in Ōkere Arm and Te Ākau, Lake Rotoiti, respectively. This method also distinguished differences in size structure and biomass between sites and provided information on sex ratios, egg-bearing and moulting. The development of the tau kōura thus enabled research and monitoring of lake kōura populations that may have not previously been representatively sampled and have generally been little studied in New Zealand despite their ecological and cultural significance.
The tau kōura was used to examine population dynamics of kōura, along a eutrophication gradient in seven Te Arawa lakes, in April, July and November 2009. Mean catch per unit effort (CPUE) and depth distribution of kōura were influenced by the combined effects of lake bed sediments, lake morphology, and hypolimnetic conditions related to trophic state. Although limited by the number of lakes that I was able to characterise, my data indicates that lake bed substrate (median sediment particle size) had a stronger influence on population characteristics than the level of enrichment/primary production as indexed by chlorophyll a (Chl-a). Nevertheless, the negative correlations between kōura abundance, with sediment carbon to nitrogen ratio (C/N), and the positive correlation between abundance and Chl-a, suggest that lake productivity does influence kōura. This component of the study indicates that eutrophication has reduced available kōura habitat in the Te Arawa lakes, particularly those that are sheltered, steep-sided and have fine lake bed sediments (with the Rotomahana mud tephra being particularly important). Lake bed substrate composition represented by sediment particle size is therefore a key factor to consider when selecting tau kōura sites for research, monitoring, restoration and harvesting, and when estimating kōura stocks in lakes. I concluded that measures to improve water quality in the Te Arawa lakes should benefit kōura populations by increasing the amount of oxygenated habitat available in the summer and autumn. 
Kōura support important customary fisheries for iwi in some Te Arawa lakes, particularly Rotoiti, Rotomā and Tarawera. However, until recently, there was limited published biological information to provide a basis for fisheries regulations. This knowledge gap has resulted in the adoption of conservative fisheries regulations and management policies by the fishery managers, the Te Arawa Lakes Trust (TALT) and Ministry of Primary Industries (MPI). A further objective of the research was therefore to examine the biological traits of lake kōura and to consider implications of these traits on the current fishing regulations and sustainable management of kōura populations in the Te Arawa lakes. 
From a review of past literature and the research findings from this study, it can be concluded that kōura populations in the Te Arawa lakes are currently not over-exploited due mostly to a low number participating in harvesting (almost exclusively Te Arawa) and because commercial harvesting is prohibited. However, the TALT wishes to encourage the revitalisation of traditional fishing practices (e.g., tau kōura) while adhering to the principles of kaitiakitanga ‒ the sustainable protection of resources. The establishment of sustainable management policies and regulations adheres to the principles of kaitiakitanga.
A number of management changes arising from the information collected in this study are suggested to protect and enhance the kōura fishery in the future. These are (1) set a slot limit with minimum size limit of 28 mm OCL and a maximum size limit of 39 mm OCL, (2) prohibit the taking of egg-bearing females, (3) limit deep-water harvest methods to the use of the tau kōura, and (4) implementing a tau kōura harvest season beginning on 1 December and ending on 31 March. These measures will protect breeding females if they are captured and the closed season will allow the majority of females to breed and release their young prior to fishing activity. Improving water quality (and thus increasing available kōura habitat) and preventing the introduction of predatory fish species such as eels (Anguilla spp.), catfish (Ameiurus nebulosus), and perch (Perca fluviatilis), that are efficient predators of kōura, are of the utmost importance in ensuring the sustainability of kōura populations in the Te Arawa lakes.

year: 2015