title: Clinical-view versus ELM: an investigation into image types in the context of skin lesion screening

authors: Day, Greg R.

abstract: Melanoma, the most serious form of skin cancer, is increasing in incidence in countries with predominantly white skinned populations. Automated tools have been proposed to help detect this most visible of cancers. Current automated systems for detecting melanoma analyse images of skin lesions for relevant image features, and classify the images based on those features. There are two types of image available to be used in such systems, Clinical-view or Epiluminescent microscopy (ELM) images. ELM images reportedly allow more accurate assessment of skin lesions in the clinical setting, but this finding has not been proven in the context of an automated system. 

This research has evaluated the question of Clinical-view versus ELM images in an automated screening system. Two methods of implementing a screening system were considered in this research. Firstly, the ‘diagnosis system’, which is based on previous work in this field, and secondly, a ‘dermatologist assessment system’, which is an original method of implementing an automated screening system. The Clinical-view versus ELM question was considered for both of these systems. 

Specifically, two automated systems were developed. The first analysed Clinical-view images, while the second processed ELM images. From the analysis, each system attempted to classify lesion images into two groups. For the diagnosis problem, the lesion was either ‘melanoma’ or ‘benign’. For the ‘dermatologist assessment’ problem, the groups were ‘excised’ or ‘not excised’. The results raise doubts over the current emphasis on ELM images in the automated diagnosis case. Similarly, it appears that Clinical-view images are of more use for reproducing ‘dermatologists assessment’. We have also shown that the ‘dermatologist assessment’ approach to screening skin lesions is a viable and potentially useful alternative to the current emphasis on the diagnosis approach.

text: Clinical-view versus ELM: an investigation into image types in the context of skin lesion screening Melanoma, the most serious form of skin cancer, is increasing in incidence in countries with predominantly white skinned populations. Automated tools have been proposed to help detect this most visible of cancers. Current automated systems for detecting melanoma analyse images of skin lesions for relevant image features, and classify the images based on those features. There are two types of image available to be used in such systems, Clinical-view or Epiluminescent microscopy (ELM) images. ELM images reportedly allow more accurate assessment of skin lesions in the clinical setting, but this finding has not been proven in the context of an automated system. 

This research has evaluated the question of Clinical-view versus ELM images in an automated screening system. Two methods of implementing a screening system were considered in this research. Firstly, the ‘diagnosis system’, which is based on previous work in this field, and secondly, a ‘dermatologist assessment system’, which is an original method of implementing an automated screening system. The Clinical-view versus ELM question was considered for both of these systems. 

Specifically, two automated systems were developed. The first analysed Clinical-view images, while the second processed ELM images. From the analysis, each system attempted to classify lesion images into two groups. For the diagnosis problem, the lesion was either ‘melanoma’ or ‘benign’. For the ‘dermatologist assessment’ problem, the groups were ‘excised’ or ‘not excised’. The results raise doubts over the current emphasis on ELM images in the automated diagnosis case. Similarly, it appears that Clinical-view images are of more use for reproducing ‘dermatologists assessment’. We have also shown that the ‘dermatologist assessment’ approach to screening skin lesions is a viable and potentially useful alternative to the current emphasis on the diagnosis approach.

year: 2000

title: Treeline vegetation composition, structure and dynamics across the AD 1655 Burrell Lapilli deposit, Mt Taranaki, New Zealand

authors: Efford, Jackson Tai

subjects: Mt Taranaki

abstract: Research was conducted on Mt Taranaki, North Island, New Zealand, to examine how the composition, structure and dynamics of treeline vegetation has been influenced by the AD 1655 Burrell Lapilli eruption. Treeline is considered as “the connecting line between the uppermost forest patches on the mountain, with trees upright and at least 3 m in height and growing in groups”. The Burrell Lapilli was deposited at a thickness of 1–40 cm over c. 150 km² of the eastern flanks of Mt Taranaki, and is thought to have inflicted widespread mechanical and chemical damage to vegetation at the time of eruption. Isopach maps of the Burrell Lapilli distribution reveal an eruption axis exists south-eastwards from the summit towards somewhere between Dawson Falls and Stratford Mountain House; out from which the thickness of lapilli decreases in all directions.

Vegetation at the treeline position (c. 1000–1100 m above sea level) was measured across this lapilli distribution with thirty-five 10 × 15 m quadrats and six variable length 5 × 35–120 m belt transects. An additional three quadrats were located on the treeline of the adjoining Pouakai Range, an area which has not suffered any recent volcanic disturbance. Across the survey area on Mt Taranaki, winter (24/7/2011–17/10/2011) temperature measurements were recorded using eighteen micro data loggers. The light requirements of selected treeline species (juveniles) were quantified in situ using canopy openness measurements made with hemispherical photography, in order to gain an insight into how species may have responded to increased light levels associated with vegetation damage by the Burrell Lapilli.
Daily average minimum temperatures ranged from 0.64–1.26 °C, average daily maximum temperatures ranged from 5.37–7.24 °C, and average daily means ranged from 3.07–3.71 °C. No major temperature anomalies were detected across the survey area.
Within the quadrats, a total of 57 vascular taxa were identified, all of which were indigenous and typical of either montane forest or shrubland vegetation types on the mountain. Quadrats were grouped based on the thickness of the Burrell Lapilli at the sites; quadrats where lapilli was 20–40 cm thick are referred to as ‘severe’, those with lapilli 1–20 cm thick as ‘minor’, and those outside the distribution of lapilli on Mt Taranaki as ‘outside’. Total basal area of trees >2 cm diameter at ground height (dgh) increased progressively from 165 to 265 m² ha⁻¹ across the severe, minor, outside, and Pouakai Range quadrat groups. Total density of trees displayed the inverse trend, with higher stocking rates in the severe (6615 stems ha⁻¹) and minor (8370 stems ha⁻¹) groups, compared with the outside (5422 stems ha⁻¹) and Pouakai Range (5822 stems ha⁻¹) groups.
The contributions of four potential canopy/emergent species (Podocarpus hallii, Griselinia littoralis, Libocedrus bidwillii, Weinmannia racemosa) varied markedly at the treeline. Across the severe, minor, outside and Pouakai Range groups, basal area of Podocarpus was 30, 40, 26 and 20 m² ha⁻¹ respectively; Griselinia was 57, 58, 52, 6 m² ha⁻¹; Libocedrus was 10, 22, 93, 7 m² ha⁻¹ and Weinmannia was 0, 1, 24, 161 m² ha⁻¹. Vegetation of each group was accordingly classified as:
Severe: Podocarpus / Griselinia scrub
Minor: Podocarpus – Libocedrus / Griselinia scrub
Outside: Libocedrus – Podocarpus / Griselinia – Weinmannia scrub
Pouakai Range: Podocarpus / Weinmannia scrub
Belt transect surveys across the treeline ecotone revealed that maximum tree diameters decreased markedly (c. 100 to 30 cm dgh) with increased elevation. Maximum tree heights also decreased with elevation, with emergent Libocedrus (c. 13 m) capable of attaining greater heights than emergent Podocarpus (c. 8 m) near the treeline position. Spatial configuration of trees implied that large canopy trees suppressed the number and size of stems in close proximity, and in areas away from canopy trees, clusters of smaller stems occurred (predominantly Pseudowintera colorata and Coprosma tenuifolia).
Common treeline species were ranked in order from most shade-tolerant to least shade-tolerant (i.e., light demanding) using the 10th percentile of the distribution of light environments occupied by each species as an approximation of the minimum light levels tolerated: Coprosma tenuifolia > Pseudowintera colorata > Raukaua simplex > Griselinia > Podocarpus > Weinmannia > Libocedrus. Consequently, diameter frequency distributions of light demanding species tended to display cohort population structures, implying they were incapable of regenerating below a closed canopy; while more shade-tolerant species displayed all-sized or reverse “J” structures, indicating their ability to regenerate continuously.
It is speculated that Libocedrus, being a tall emergent, was eliminated from the most severely affected areas because it suffered a direct impact from the lapilli and has poor resprouting capabilities. It did not successfully regenerate there because (1) seed dispersal did not occur, (2) it was competitively excluded, (3) or it could not tolerate the new substrate. Where the effects of the eruption were less severe, Libocedrus was more successful, with an even-aged population initiated due to the increased light levels on the forest floor. Griselinia was most successful in areas severely affected by the eruption, probably because it could establish epiphytically on brightly lit snags well before suitable substrate developed. Griselinia has maintained its dominance due to its in situ mode of regeneration, whereby seedlings establish epiphytically in parent trees, combined with its ability to basally resprout. Weinmannia was not capable of capitalising on the severely affected areas in the same way, because at this elevation it is very close to its upper altitudinal limit, and would not have tolerated exposure associated with open sites; then, following canopy closure, light levels would have been too low for it to establish. Podocarpus, being a more shade-tolerant species, probably established within the eruption zone sometime after the event, and continues to regenerate below a closed canopy. Seedling and sapling data suggest that in the absence of severe disturbance, the compositional differences observed around the treeline of Mt Taranaki are likely to persist.
The explanation of vegetation patterns resulting from tephra eruptions elsewhere in the world may benefit from the findings that (1) emergent species suffer the most deleterious effects during a tephra eruption, (2) epiphytic regeneration may be an important mechanism for early arrivals into devastated areas, (3) light demanding species thrive as a result of openings created in the canopy, and (4) the successional trajectory of affected areas could be altered to the extent that vegetation patterns across tephra deposits may persist indefinitely.

text: Treeline vegetation composition, structure and dynamics across the AD 1655 Burrell Lapilli deposit, Mt Taranaki, New Zealand Research was conducted on Mt Taranaki, North Island, New Zealand, to examine how the composition, structure and dynamics of treeline vegetation has been influenced by the AD 1655 Burrell Lapilli eruption. Treeline is considered as “the connecting line between the uppermost forest patches on the mountain, with trees upright and at least 3 m in height and growing in groups”. The Burrell Lapilli was deposited at a thickness of 1–40 cm over c. 150 km² of the eastern flanks of Mt Taranaki, and is thought to have inflicted widespread mechanical and chemical damage to vegetation at the time of eruption. Isopach maps of the Burrell Lapilli distribution reveal an eruption axis exists south-eastwards from the summit towards somewhere between Dawson Falls and Stratford Mountain House; out from which the thickness of lapilli decreases in all directions.

Vegetation at the treeline position (c. 1000–1100 m above sea level) was measured across this lapilli distribution with thirty-five 10 × 15 m quadrats and six variable length 5 × 35–120 m belt transects. An additional three quadrats were located on the treeline of the adjoining Pouakai Range, an area which has not suffered any recent volcanic disturbance. Across the survey area on Mt Taranaki, winter (24/7/2011–17/10/2011) temperature measurements were recorded using eighteen micro data loggers. The light requirements of selected treeline species (juveniles) were quantified in situ using canopy openness measurements made with hemispherical photography, in order to gain an insight into how species may have responded to increased light levels associated with vegetation damage by the Burrell Lapilli.
Daily average minimum temperatures ranged from 0.64–1.26 °C, average daily maximum temperatures ranged from 5.37–7.24 °C, and average daily means ranged from 3.07–3.71 °C. No major temperature anomalies were detected across the survey area.
Within the quadrats, a total of 57 vascular taxa were identified, all of which were indigenous and typical of either montane forest or shrubland vegetation types on the mountain. Quadrats were grouped based on the thickness of the Burrell Lapilli at the sites; quadrats where lapilli was 20–40 cm thick are referred to as ‘severe’, those with lapilli 1–20 cm thick as ‘minor’, and those outside the distribution of lapilli on Mt Taranaki as ‘outside’. Total basal area of trees >2 cm diameter at ground height (dgh) increased progressively from 165 to 265 m² ha⁻¹ across the severe, minor, outside, and Pouakai Range quadrat groups. Total density of trees displayed the inverse trend, with higher stocking rates in the severe (6615 stems ha⁻¹) and minor (8370 stems ha⁻¹) groups, compared with the outside (5422 stems ha⁻¹) and Pouakai Range (5822 stems ha⁻¹) groups.
The contributions of four potential canopy/emergent species (Podocarpus hallii, Griselinia littoralis, Libocedrus bidwillii, Weinmannia racemosa) varied markedly at the treeline. Across the severe, minor, outside and Pouakai Range groups, basal area of Podocarpus was 30, 40, 26 and 20 m² ha⁻¹ respectively; Griselinia was 57, 58, 52, 6 m² ha⁻¹; Libocedrus was 10, 22, 93, 7 m² ha⁻¹ and Weinmannia was 0, 1, 24, 161 m² ha⁻¹. Vegetation of each group was accordingly classified as:
Severe: Podocarpus / Griselinia scrub
Minor: Podocarpus – Libocedrus / Griselinia scrub
Outside: Libocedrus – Podocarpus / Griselinia – Weinmannia scrub
Pouakai Range: Podocarpus / Weinmannia scrub
Belt transect surveys across the treeline ecotone revealed that maximum tree diameters decreased markedly (c. 100 to 30 cm dgh) with increased elevation. Maximum tree heights also decreased with elevation, with emergent Libocedrus (c. 13 m) capable of attaining greater heights than emergent Podocarpus (c. 8 m) near the treeline position. Spatial configuration of trees implied that large canopy trees suppressed the number and size of stems in close proximity, and in areas away from canopy trees, clusters of smaller stems occurred (predominantly Pseudowintera colorata and Coprosma tenuifolia).
Common treeline species were ranked in order from most shade-tolerant to least shade-tolerant (i.e., light demanding) using the 10th percentile of the distribution of light environments occupied by each species as an approximation of the minimum light levels tolerated: Coprosma tenuifolia > Pseudowintera colorata > Raukaua simplex > Griselinia > Podocarpus > Weinmannia > Libocedrus. Consequently, diameter frequency distributions of light demanding species tended to display cohort population structures, implying they were incapable of regenerating below a closed canopy; while more shade-tolerant species displayed all-sized or reverse “J” structures, indicating their ability to regenerate continuously.
It is speculated that Libocedrus, being a tall emergent, was eliminated from the most severely affected areas because it suffered a direct impact from the lapilli and has poor resprouting capabilities. It did not successfully regenerate there because (1) seed dispersal did not occur, (2) it was competitively excluded, (3) or it could not tolerate the new substrate. Where the effects of the eruption were less severe, Libocedrus was more successful, with an even-aged population initiated due to the increased light levels on the forest floor. Griselinia was most successful in areas severely affected by the eruption, probably because it could establish epiphytically on brightly lit snags well before suitable substrate developed. Griselinia has maintained its dominance due to its in situ mode of regeneration, whereby seedlings establish epiphytically in parent trees, combined with its ability to basally resprout. Weinmannia was not capable of capitalising on the severely affected areas in the same way, because at this elevation it is very close to its upper altitudinal limit, and would not have tolerated exposure associated with open sites; then, following canopy closure, light levels would have been too low for it to establish. Podocarpus, being a more shade-tolerant species, probably established within the eruption zone sometime after the event, and continues to regenerate below a closed canopy. Seedling and sapling data suggest that in the absence of severe disturbance, the compositional differences observed around the treeline of Mt Taranaki are likely to persist.
The explanation of vegetation patterns resulting from tephra eruptions elsewhere in the world may benefit from the findings that (1) emergent species suffer the most deleterious effects during a tephra eruption, (2) epiphytic regeneration may be an important mechanism for early arrivals into devastated areas, (3) light demanding species thrive as a result of openings created in the canopy, and (4) the successional trajectory of affected areas could be altered to the extent that vegetation patterns across tephra deposits may persist indefinitely.

year: 2012

title: Boat electrofishing survey of fish abundance in the Ohau Channel, Rotorua, in 2013

authors: Hicks, Brendan J.

abstract: The aim of this survey was to provide on-going monitoring of the fish communities and abundance in the Ohau Channel, especially fish species that are taonga to Maori (eels, goldfish, and koura). In the current study we present the findings from the seventh year of sampling (2013) in view of previous surveys using boat electrofishing in the Ohau Channel. 
We used the University of Waikato's 4.5 m-long, aluminium-hulled electrofishing boat to catch a total of 1,025 fish (20.3 kg) from 11 sites comprising 2,817 lineal m and 11,484 m² in area on 27 November 2013. Common bully were the most abundant fish species (57% of the catch) followed by common smelt (36% of the catch).
Goldfish had their highest biomasses in the lower channel, especially at site 10 near Lake Rotoiti (up to 7.25 g m⁻²). Catch per unit effort (CPUE) for common bullies exceeded smelt CPUE at all sites except site 1, reflecting their greater densities. CPUE for rainbow trout was variable between the sites, and greatest at site 3. 
The abundance of common bullies in 2013 reversed the apparent trend of reducing abundance since these surveys started in 2007. The cause of fluctuating bully abundance is not known, and was not accounted for by water clarity expressed as black disc distance (BDD) or water conductivity. Poor water clarity can reduce the efficiency of electrofishing, but BDD was greater in 2012 than in 2011 when common bully densities were lower. In 2013, the apparent decline in smelt abundance was also reversed, but the relatively inefficient sampling resulting from boat electrofishing for these two species should be considered. 
The increased goldfish biomass in 2011-2013 arose because of targeted fishing in the excavated side branch, which clearly offers good habitat for goldfish. Removal of goldfish in the previous years may have reduced the density in the excavated side channel (site 11) compared to previous years. In 2013, a shortfin eel was caught, following the first shortfin eel encountered in the Ohau Channel in 2012.

text: Boat electrofishing survey of fish abundance in the Ohau Channel, Rotorua, in 2013 The aim of this survey was to provide on-going monitoring of the fish communities and abundance in the Ohau Channel, especially fish species that are taonga to Maori (eels, goldfish, and koura). In the current study we present the findings from the seventh year of sampling (2013) in view of previous surveys using boat electrofishing in the Ohau Channel. 
We used the University of Waikato's 4.5 m-long, aluminium-hulled electrofishing boat to catch a total of 1,025 fish (20.3 kg) from 11 sites comprising 2,817 lineal m and 11,484 m² in area on 27 November 2013. Common bully were the most abundant fish species (57% of the catch) followed by common smelt (36% of the catch).
Goldfish had their highest biomasses in the lower channel, especially at site 10 near Lake Rotoiti (up to 7.25 g m⁻²). Catch per unit effort (CPUE) for common bullies exceeded smelt CPUE at all sites except site 1, reflecting their greater densities. CPUE for rainbow trout was variable between the sites, and greatest at site 3. 
The abundance of common bullies in 2013 reversed the apparent trend of reducing abundance since these surveys started in 2007. The cause of fluctuating bully abundance is not known, and was not accounted for by water clarity expressed as black disc distance (BDD) or water conductivity. Poor water clarity can reduce the efficiency of electrofishing, but BDD was greater in 2012 than in 2011 when common bully densities were lower. In 2013, the apparent decline in smelt abundance was also reversed, but the relatively inefficient sampling resulting from boat electrofishing for these two species should be considered. 
The increased goldfish biomass in 2011-2013 arose because of targeted fishing in the excavated side branch, which clearly offers good habitat for goldfish. Removal of goldfish in the previous years may have reduced the density in the excavated side channel (site 11) compared to previous years. In 2013, a shortfin eel was caught, following the first shortfin eel encountered in the Ohau Channel in 2012.

year: 2014