Image analysis from TEM and AFM micrograph, Table S1, S2, S3, Figure S1, Figure S2

We report on metal enrichment along a natural pH gradient owing to increased CO2 degassing at cold, shal- low seeps of Vulcano Island in the Mediterranean Sea, off Sicily. We assessed composition of unfiltered and filtered seawater (b100 nm) along acidic zones ranging between ambient and pH 5, and showed that most seep derived elements are present as nanoclusters which then aggregate into larger colloids while mixing with ambient seawater along a pH gradient. Size and elemental composition of such naturally occurring nanoparticles assessed by modern characterisation methods were in good agreement with the results from conventional analytical methods. We provide analytical evidence for the presence in the water column of a large fraction of seep derived ele- ments (e.g. approximately 50% of iron, over 80% of Mn, 100% of Cr, S and Zn) in the form of nano sized par- ticles (e.g. b100 nm) even at typical open ocean pHs. We launch in situ sampling protocols and sample preparation procedures for multi-method suitable to obtain accurate measurements on nanoparticles from environmental samples. Based on our results a first insight to the formation of natural nanoparticles at cold CO2 seeps is presented and the persistence of such nano-clusters in the surrounding seawater is stipulated.

Icebergs in the Amundsen Sea (Antarctica) determined from ENVISAT ASAR WSM data using object-based image analysis approach, link to ESRI GDB files

ENVISAT ASAR WSM images with pixel size 150 × 150 m, acquired in different meteorological, oceanographic and sea ice conditions were used to determined icebergs in the Amundsen Sea (Antarctica). An object-based method for automatic iceberg detection from SAR data has been developed and applied. The object identification is based on spectral and spatial parameters on 5 scale levels, and was verified with manual classification in four polygon areas, chosen to represent varying environmental conditions. The algorithm works comparatively well in freezing temperatures and strong wind conditions, prevailing in the Amundsen Sea during the year. The detection rate was 96% which corresponds to 94% of the area (counting icebergs larger than 0.03 km**2), for all seasons. The presented algorithm tends to generate errors in the form of false alarms, mainly caused by the presence of ice floes, rather than misses. This affects the reliability since false alarms were manually corrected post analysis.

Benthic cover map of Heron Reef derived from a high-spatial-resolution multi-spectral satellite image using object based image analysis

Providing accurate maps of coral reefs where the spatial scale and labels of the mapped features correspond to map units appropriate for examining biological and geomorphic structures and processes is a major challenge for remote sensing. The objective of this work is to assess the accuracy and relevance of the process used to derive geomorphic zone and benthic community zone maps for three western Pacific coral reefs produced from multi-scale, object-based image analysis (OBIA) of high-spatial-resolution multi-spectral images, guided by field survey data. Three Quickbird-2 multi-spectral data sets from reefs in Australia, Palau and Fiji and georeferenced field photographs were used in a multi-scale segmentation and object-based image classification to map geomorphic zones and benthic community zones. A per-pixel approach was also tested for mapping benthic community zones. Validation of the maps and comparison to past approaches indicated the multi-scale OBIA process enabled field data, operator field experience and a conceptual hierarchical model of the coral reef environment to be linked to provide output maps at geomorphic zone and benthic community scales on coral reefs. The OBIA mapping accuracies were comparable with previously published work using other methods; however, the classes mapped were matched to a predetermined set of features on the reef.

Core scan image analysis corrected for cracks, ODP Hole 154-926C

Drill cores are essential for the study of deep-sea sediments and on-land sites because often no suitable outcrop is available or accessible. These cores form the backbone of stratigraphical studies using and combining various dating techniques. Cyclostratigraphy is usually based on fast and inexpensive measurements of physical sediment properties. One indirect but highly valuable proxy for reconstructing the sediment composition and variability is sediment color. However, cracks and other disturbances in sediment cores may dramatically influence the quality of color data retrieved either directly from photospectrometry or derived from core image analysis. Here we present simple but powerful algorithms to extract color data from core images, and focus on routines to exclude cracks from these images. Results are discussed using the example of an ODP core from the Ceara Rise in the Central Atlantic. The crack correction approach presented highly improves the quality of color data and allows the easy incorporation of cracked cores into studies based on core images. This facilitates the quick and inexpensive generation of large color datasets directly from quantified core images, for cyclostratigraphy and other purposes.

Coral reef habitat maps derived from a high-spatial-resolution multi-spectral satellite image using object based image analysis

Coral reef maps at various spatial scales and extents are needed for mapping, monitoring, modelling, and management of these environments. High spatial resolution satellite imagery, pixel <10 m, integrated with field survey data and processed with various mapping approaches, can provide these maps. These approaches have been accurately applied to single reefs (10-100 km**2), covering one high spatial resolution scene from which a single thematic layer (e.g. benthic community) is mapped. This article demonstrates how a hierarchical mapping approach can be applied to coral reefs from individual reef to reef-system scales (10-1000 km**2) using object-based image classification of high spatial resolution images guided by ecological and geomorphological principles. The approach is demonstrated for three individual reefs (10-35 km**2) in Australia, Fiji, and Palau; and for three complex reef systems (300-600 km**2) one in the Solomon Islands and two in Fiji. Archived high spatial resolution images were pre-processed and mosaics were created for the reef systems. Georeferenced benthic photo transect surveys were used to acquire cover information. Field and image data were integrated using an object-based image analysis approach that resulted in a hierarchically structured classification. Objects were assigned class labels based on the dominant benthic cover type, or location-relevant ecological and geomorphological principles, or a combination thereof. This generated a hierarchical sequence of reef maps with an increasing complexity in benthic thematic information that included: 'reef', 'reef type', 'geomorphic zone', and 'benthic community'. The overall accuracy of the 'geomorphic zone' classification for each of the six study sites was 76-82% using 6-10 mapping categories. For 'benthic community' classification, the overall accuracy was 52-75% with individual reefs having 14-17 categories and reef systems 20-30 categories. We show that an object-based classification of high spatial resolution imagery, guided by field data and ecological and geomorphological principles, can produce consistent, accurate benthic maps at four hierarchical spatial scales for coral reefs of various sizes and complexities.

A stereo-image analysis JAVA software with links to executable and source code

Scientists planning to use underwater stereoscopic image technologies are often faced with numerous problems during the methodological implementations: commercial equipment is too expensive; the setup or calibration is too complex; or the imaging processing (i.e. measuring objects in the stereo-images) is too complicated to be performed without a time-consuming phase of training and evaluation. The present paper addresses some of these problems and describes a workflow for stereoscopic measurements for marine biologists. It also provides instructions on how to assemble an underwater stereo-photographic system with two digital consumer cameras and gives step-by-step guidelines for setting up the hardware. The second part details a software procedure to correct stereo-image pairs for lens distortions, which is especially important when using cameras with non-calibrated optical units. The final part presents a guide to the process of measuring the lengths (or distances) of objects in stereoscopic image pairs. To reveal the applicability and the restrictions of the described systems and to test the effects of different types of camera (a compact camera and an SLR type), experiments were performed to determine the precision and accuracy of two generic stereo-imaging units: a diver-operated system based on two Olympus Mju 1030SW compact cameras and a cable-connected observatory system based on two Canon 1100D SLR cameras. In the simplest setup without any correction for lens distortion, the low-budget Olympus Mju 1030SW system achieved mean accuracy errors (percentage deviation of a measurement from the object's real size) between 10.2 and -7.6% (overall mean value: -0.6%), depending on the size, orientation and distance of the measured object from the camera. With the single lens reflex (SLR) system, very similar values between 10.1% and -3.4% (overall mean value: -1.2%) were observed. Correction of the lens distortion significantly improved the mean accuracy errors of either system. Even more, system precision (spread of the accuracy) improved significantly in both systems. Neither the use of a wide-angle converter nor multiple reassembly of the system had a significant negative effect on the results. The study shows that underwater stereophotography, independent of the system, has a high potential for robust and non-destructive in situ sampling and can be used without prior specialist training.