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    A quantitative comparison of towed-camera and diver-camera transects for monitoring coral reefs
    (PeerJ Inc., 2021) Cresswell AK; Ryan NM; Heyward AJ; Smith ANH; Colquhoun J; Case M; Birt MJ; Chinkin M; Wyatt M; Radford B; Costello P; Gilmour JP; Toonen R
    Novel tools and methods for monitoring marine environments can improve efficiency but must not compromise long-term data records. Quantitative comparisons between new and existing methods are therefore required to assess their compatibility for monitoring. Monitoring of shallow water coral reefs is typically conducted using diver-based collection of benthic images along transects. Diverless systems for obtaining underwater images (e.g. towed-cameras, remotely operated vehicles, autonomous underwater vehicles) are increasingly used for mapping coral reefs. Of these imaging platforms, towed-cameras offer a practical, low cost and efficient method for surveys but their utility for repeated measures in monitoring studies has not been tested. We quantitatively compare a towed-camera approach to repeated surveys of shallow water coral reef benthic assemblages on fixed transects, relative to benchmark data from diver photo-transects. Differences in the percent cover detected by the two methods was partly explained by differences in the morphology of benthic groups. The reef habitat and physical descriptors of the site-slope, depth and structural complexity-also influenced the comparability of data, with differences between the tow-camera and the diver data increasing with structural complexity and slope. Differences between the methods decreased when a greater number of images were collected per tow-camera transect. We attribute lower image quality (variable perspective, exposure and focal distance) and lower spatial accuracy and precision of the towed-camera transects as the key reasons for differences in the data from the two methods and suggest changes to the sampling design to improve the application of tow-cameras to monitoring.
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    Development of a low-cost automated sample presentation and analysis system for counting and classifying nematode eggs : a thesis presented in partial fulfilment of the requirements for the degree of Master of Engineering in Mechatronics at Massey University, Manawatu, New Zealand
    (Massey University, 2017) Pedersen, Benjamin
    This thesis discusses the concept development and design of a low-cost, automated, sample presentation system for faecal egg counting, and classification. The system developed uses microfluidics to present nematode eggs for digital imaging to produce images suitable for image analysis and classification. The system costs are kept low by using simple manufacturing methods and commonly available equipment to produce microfluidic counting chambers, which can be interfaced with conventional microscopes. This thesis includes details of the design and implementation of the software developed to allow capture and processing of images from the presentation system. This thesis also includes details on the measures taken to correct for the optical aberrations introduced by the sample presentation system.
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    An investigation into the use of video image analysis (VIA) and visible-near infrared (NIR) spectroscopy for carcase evaluation : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Palmerston North, New Zealand
    (Massey University, 2012) Craigie, Cameron Ross
    In order for the meat industry to move towards a carcase payment system that is more consumer-focused, there is a need to identify carcases that have a higher yield of superior eating quality meat. Through a series of experiments, this thesis investigates the relationships between video image analysis (VIA) variables and saleable meat yield (SMY%) of high-value cuts in beef carcases, and also the relationships between visible-near infrared (NIR) spectra and instrumental meat quality parameters in beef, lamb and venison of various breeds and genders. Results showed that VIA could effectively replace the visual classifier for classifying beef carcases according to the EUROP carcase classification system, and that both visual and VIA systems showed some promise for predicting the yield of high-value sirloin yield through the EUROP-grid information. Both VIA and visual systems could only account for approximately 57% of the variation in sirloin SMY%, but the relationship between SMY% and other possible VIA outputs such as lengths, widths and volumes remains largely uncharacterized. Instrumental measures of meat quality (shear force, pH and colour) of M. longissimus thoracis et lumborum (LTL) from 234 beef carcases and 208 Texel lambs showed that gender had a larger effect on meat quality than breed. Data from these two experiments was used to determine the relationship between NIR spectra and instrumental meat quality parameters in beef and lamb LTL. NIR showed promise for identifying beef with high ultimate pH values and lamb with high intramuscular fat percentages, but the prediction of shear force using NIR spectra in both beef and lamb was less accurate. The effects on meat quality of sex, breed, chilled aging and location within venison M. Longissimus lumborum, for samples from 79 farmed deer showed that all factors influenced venison meat quality, with aging time and gender having the largest effects. The relationships between NIR spectra and venison meat quality indicated that NIR spectra could be used to identify samples with high ultimate pH and high shear force values.