title: Simple stereo matching algorithm for localising keypoints in a restricted search space

authors: Seabright, Matthew

abstract: Modern stereo matching algorithms generally rely on matching image features such as colour and texture to find corresponding matches between images. They can provide very good results but be very computationally intensive. However, in cases where the objects to be localised lie approximately on a known plane, a much simpler algorithm can be applied. One such case is localising kiwifruit in modern orchards, as the plants are trained to grow in a planar structure known as a pergola. The proposed algorithm uses tight distance limits (based on orchard geometry) to reduce the search space for matching fruit to a small window. For the majority of kiwifruit, the search window is small enough to contain only one fruit in the adjacent image, giving only a single solution. In cases where there are tightly grouped fruit or false positive fruit detections adjacent to true positive fruit detections, there can be multiple potential matching solutions. To solve these, each potential solution is evaluated based on how closely it conforms to the mean object distance from camera and a solution is selected. On real world test data containing 121 image pairs, the algorithm has a 99.2 % true positive rate. Computation time was 1.97 ms per image pair.

text: Simple stereo matching algorithm for localising keypoints in a restricted search space Modern stereo matching algorithms generally rely on matching image features such as colour and texture to find corresponding matches between images. They can provide very good results but be very computationally intensive. However, in cases where the objects to be localised lie approximately on a known plane, a much simpler algorithm can be applied. One such case is localising kiwifruit in modern orchards, as the plants are trained to grow in a planar structure known as a pergola. The proposed algorithm uses tight distance limits (based on orchard geometry) to reduce the search space for matching fruit to a small window. For the majority of kiwifruit, the search window is small enough to contain only one fruit in the adjacent image, giving only a single solution. In cases where there are tightly grouped fruit or false positive fruit detections adjacent to true positive fruit detections, there can be multiple potential matching solutions. To solve these, each potential solution is evaluated based on how closely it conforms to the mean object distance from camera and a solution is selected. On real world test data containing 121 image pairs, the algorithm has a 99.2 % true positive rate. Computation time was 1.97 ms per image pair.

year: 2018

title: Grainyhead-like 2 is required for morphological integrity of mouse embryonic stem cells and orderly formation of inner ear-like organoids

authors: Forrester-Gauntlett, Blaise

abstract: Mutations in the transcription factor gene grainyhead-like 2 (GRHL2) are associated with progressive non-syndromic sensorineural deafness autosomal dominant type 28 (DFNA28) in humans. Since complete loss of Grhl2 is lethal in mouse embryos, we studied its role during inner ear pathology and hearing loss in vitro. To this end, we generated different homozygous deletions to knockout Grhl2 in mouse embryonic stem cells (Grhl2-KO ESCs), including some mimicking naturally occurring truncations in the dimerisation domain related to human DFNA28. Under naïve culture conditions, Grhl2-KO cells in suspension were more heterogenous in size and larger than wild-type controls. Adherent Grhl2-KO cells were also larger, with a less uniform shape, flattened, less circular morphology, forming loose monolayer colonies with poorly defined edges. These changes correlated with lower expression of epithelial cadherin Cdh1 but no changes in tight junction markers (Ocln, Tjp2) or other Grhl isoforms (Grhl1, Grhl3). Clonogenicity from single cells, proliferation rates of cell populations and proliferation markers were reduced in Grhl2-KO ESCs. We next induced stepwise directed differentiation of Grhl2-KO ESCs along an otic pathway, giving rise to three-dimensional inner ear-like organoids (IELOs). Quantitative morphometry revealed that Grhl2-KO cells initially formed larger IELOs with a less compacted structure, more eccentric shape and increased surface area. These morphological changes persisted for up to one week. They were partially rescued by forced cell aggregation and fully restored by stably overexpressing exogenous Grhl2 in Grhl2-KO ESCs, indicating that Grhl2 alters cell-cell interactions. On day 8, aggregates were transferred into minimal maturation medium to allow self-guided organogenesis for another two weeks. During this period, Grhl2-KO cells and wild-type controls developed similarly, expressing neural, neuronal and sensory hair cell markers, while maintaining their initial differences in size and shape. In summary, Grhl2 is required for morphological maintenance of ESCs and orderly formation of IELOs, consistent with an essential role in organising epithelial integrity during inner ear development. Our findings validate quantitative morphometry as a useful, non-invasive screening method for molecular phenotyping of candidate mutations during organoid development.

text: Grainyhead-like 2 is required for morphological integrity of mouse embryonic stem cells and orderly formation of inner ear-like organoids Mutations in the transcription factor gene grainyhead-like 2 (GRHL2) are associated with progressive non-syndromic sensorineural deafness autosomal dominant type 28 (DFNA28) in humans. Since complete loss of Grhl2 is lethal in mouse embryos, we studied its role during inner ear pathology and hearing loss in vitro. To this end, we generated different homozygous deletions to knockout Grhl2 in mouse embryonic stem cells (Grhl2-KO ESCs), including some mimicking naturally occurring truncations in the dimerisation domain related to human DFNA28. Under naïve culture conditions, Grhl2-KO cells in suspension were more heterogenous in size and larger than wild-type controls. Adherent Grhl2-KO cells were also larger, with a less uniform shape, flattened, less circular morphology, forming loose monolayer colonies with poorly defined edges. These changes correlated with lower expression of epithelial cadherin Cdh1 but no changes in tight junction markers (Ocln, Tjp2) or other Grhl isoforms (Grhl1, Grhl3). Clonogenicity from single cells, proliferation rates of cell populations and proliferation markers were reduced in Grhl2-KO ESCs. We next induced stepwise directed differentiation of Grhl2-KO ESCs along an otic pathway, giving rise to three-dimensional inner ear-like organoids (IELOs). Quantitative morphometry revealed that Grhl2-KO cells initially formed larger IELOs with a less compacted structure, more eccentric shape and increased surface area. These morphological changes persisted for up to one week. They were partially rescued by forced cell aggregation and fully restored by stably overexpressing exogenous Grhl2 in Grhl2-KO ESCs, indicating that Grhl2 alters cell-cell interactions. On day 8, aggregates were transferred into minimal maturation medium to allow self-guided organogenesis for another two weeks. During this period, Grhl2-KO cells and wild-type controls developed similarly, expressing neural, neuronal and sensory hair cell markers, while maintaining their initial differences in size and shape. In summary, Grhl2 is required for morphological maintenance of ESCs and orderly formation of IELOs, consistent with an essential role in organising epithelial integrity during inner ear development. Our findings validate quantitative morphometry as a useful, non-invasive screening method for molecular phenotyping of candidate mutations during organoid development.

year: 2023-01-01

title: Decolonising Pākehā ways of being: Revealing third space Pākehā experiences

authors: Brown, Micheal William

subjects: Pakeha

abstract: This thesis asks two central questions. First, what kinds of experiences occur when Pākehā become interested and involved in te ao Māori (the Māori world)? Second, how might sharing of these experiences help other Pākehā better understand their relationship with Māori? The account is grounded in concepts of colonisation and the coloniser/colonised relation, Othering, Whiteness, hybridity and the third space, biculturalism, theories of movement between groups, and decolonisation. It particularly drew on Homi Bhabha’s notions of the third space to theorise and explain the process of change that occurred for 13 Pākehā involved in te ao Māori. Utilising a qualitative design based on grounded theory and in-depth interviewing the research investigated their “lived” experiences and their choice to encounter then engage with te ao Māori. It is their experiences that I interpret in this thesis as “third space Pākehā experiences”. Through my employment of grounded theory methodology to analyse the korero (stories) I collected, I argue that a transformative process of change occurred for the 13 participants because they became interested and engaged more in ongoing experiences of te ao Māori. I interpreted this process as “Pākehā decolonisation”. In my analysis I found that at the individual level decolonisation helped these Pākehā bridge gaps that emerged as “differences” between te ao Māori and te ao Pākehā which led them to develop a new and enriched understanding of themselves. Their engagement with te ao Māori produced exciting and rewarding experiences, the richness of these is revealed in the storylines. Also, their ongoing experiences moved towards effective strategies to engage in discussions with other Pākehā about te ao Māori, which were respectful to both Māori and Pākehā cultures. I interpreted this development as the “Pākehā educating Pākehā” strategy. My analysis also suggested that five key thematic elements - or what I call five “occurrences” of Pākehā decolonisation, existed within each participant’s third space experiences. They were: 1) all participants chose to engage in many diverse encounters with te ao Māori, 2) this led the individual to their discovery of ngā wairua o te ao Māori (values of the Māori world), 3) as well as to experiencing Othering experiences from Pākehā, 4) the ongoing choice to engage with te ao Māori developed into awareness and experience of sites/locations where equality between Māori and Pākehā existed and, 5) and it was through confrontational experiences that these Pākehā began to learn successful Pākehā educating Pākehā strategies which they employed when engaging with other Pākehā about te ao Māori. These five occurrences happened frequently and infrequently across participants and they occurred in multiple settings as well as during different decades of their lives. Nonetheless, the choice to enter into these experience(s), whether at the time of occurrence - or on reflection at a later stage - emerged as a defining of their “journey” into te ao Māori; a journey of enriched, insightful and meaningful experiences that helped these Pākehā develop a more sophisticated understanding of te ao Māori and their relationship to Māori within that world. Thus, these Pākehā discovered that exploration into te ao Māori was a benefit to themselves as individual Pākehā. This thesis is an applied research study that draws from Homi Bhabha’s (1994) theory/concept of hybridity and movement between groups. I employed this approach because I was concerned with movement by a group member (Pākehā) toward another group (Māori). The research conceptualises Bhabha’s (1994) “third space” as an “experience” rather than a permanent positioning and explores ways in which change occurs for non hybrid group members who engage in the third space experience and, that a third space vocabulary exists for talking about shared experiences that does not put one’s own identity at risk. The main contributions of this research are threefold. Firstly, when Pākehā enter into te ao Māori they encounter third space experiences that reveal new and enriched ways to experience te ao Māori, and they develop a more sophisticated view of the Māori and Pākehā coloniser/colonial relation, its history, as well as present relations and pathways for future equal engagement. Secondly, third space experiences offer a “way forward” for Māori and Pākehā relationships that suggests an alternative to contestation and confrontation. Third, third space experiences provide a pathway toward a Pākehā educating Pākehā strategy; an accessible and practical outcome of a positive and rewarding alternative decolonisation process which helps other Pākehā discover a deeper understanding of their place in New Zealand. I argue that decolonisation and the Pākehā educating Pākehā strategy helps Pākehā learn from their lived experiences of “being Pākehā” - a phrase coined by historian Michael King (1985, 1999b).

text: Decolonising Pākehā ways of being: Revealing third space Pākehā experiences This thesis asks two central questions. First, what kinds of experiences occur when Pākehā become interested and involved in te ao Māori (the Māori world)? Second, how might sharing of these experiences help other Pākehā better understand their relationship with Māori? The account is grounded in concepts of colonisation and the coloniser/colonised relation, Othering, Whiteness, hybridity and the third space, biculturalism, theories of movement between groups, and decolonisation. It particularly drew on Homi Bhabha’s notions of the third space to theorise and explain the process of change that occurred for 13 Pākehā involved in te ao Māori. Utilising a qualitative design based on grounded theory and in-depth interviewing the research investigated their “lived” experiences and their choice to encounter then engage with te ao Māori. It is their experiences that I interpret in this thesis as “third space Pākehā experiences”. Through my employment of grounded theory methodology to analyse the korero (stories) I collected, I argue that a transformative process of change occurred for the 13 participants because they became interested and engaged more in ongoing experiences of te ao Māori. I interpreted this process as “Pākehā decolonisation”. In my analysis I found that at the individual level decolonisation helped these Pākehā bridge gaps that emerged as “differences” between te ao Māori and te ao Pākehā which led them to develop a new and enriched understanding of themselves. Their engagement with te ao Māori produced exciting and rewarding experiences, the richness of these is revealed in the storylines. Also, their ongoing experiences moved towards effective strategies to engage in discussions with other Pākehā about te ao Māori, which were respectful to both Māori and Pākehā cultures. I interpreted this development as the “Pākehā educating Pākehā” strategy. My analysis also suggested that five key thematic elements - or what I call five “occurrences” of Pākehā decolonisation, existed within each participant’s third space experiences. They were: 1) all participants chose to engage in many diverse encounters with te ao Māori, 2) this led the individual to their discovery of ngā wairua o te ao Māori (values of the Māori world), 3) as well as to experiencing Othering experiences from Pākehā, 4) the ongoing choice to engage with te ao Māori developed into awareness and experience of sites/locations where equality between Māori and Pākehā existed and, 5) and it was through confrontational experiences that these Pākehā began to learn successful Pākehā educating Pākehā strategies which they employed when engaging with other Pākehā about te ao Māori. These five occurrences happened frequently and infrequently across participants and they occurred in multiple settings as well as during different decades of their lives. Nonetheless, the choice to enter into these experience(s), whether at the time of occurrence - or on reflection at a later stage - emerged as a defining of their “journey” into te ao Māori; a journey of enriched, insightful and meaningful experiences that helped these Pākehā develop a more sophisticated understanding of te ao Māori and their relationship to Māori within that world. Thus, these Pākehā discovered that exploration into te ao Māori was a benefit to themselves as individual Pākehā. This thesis is an applied research study that draws from Homi Bhabha’s (1994) theory/concept of hybridity and movement between groups. I employed this approach because I was concerned with movement by a group member (Pākehā) toward another group (Māori). The research conceptualises Bhabha’s (1994) “third space” as an “experience” rather than a permanent positioning and explores ways in which change occurs for non hybrid group members who engage in the third space experience and, that a third space vocabulary exists for talking about shared experiences that does not put one’s own identity at risk. The main contributions of this research are threefold. Firstly, when Pākehā enter into te ao Māori they encounter third space experiences that reveal new and enriched ways to experience te ao Māori, and they develop a more sophisticated view of the Māori and Pākehā coloniser/colonial relation, its history, as well as present relations and pathways for future equal engagement. Secondly, third space experiences offer a “way forward” for Māori and Pākehā relationships that suggests an alternative to contestation and confrontation. Third, third space experiences provide a pathway toward a Pākehā educating Pākehā strategy; an accessible and practical outcome of a positive and rewarding alternative decolonisation process which helps other Pākehā discover a deeper understanding of their place in New Zealand. I argue that decolonisation and the Pākehā educating Pākehā strategy helps Pākehā learn from their lived experiences of “being Pākehā” - a phrase coined by historian Michael King (1985, 1999b).

year: 2011