Analysis of Benthic Survey Images via CoralNet: A Summary of Standard Operating Procedures and Guidelines Paula Lozada-Misa Brett D. Schumacher Bernardo Vargas-Ángel January 2017 Administrative Report H-17-02 https://doi.org/V5/10.7289/V5/AR-PIFSC-H-17-02 About this report Pacific Islands Fisheries Science Center Administrative Reports are issued to promptly disseminate scientific and technical information to marine resource managers, scientists, and the general public. Their contents cover a range of topics, including biological and economic research, stock assessment, trends in fisheries, and other subjects. Administrative Reports typically have not been reviewed outside the Center. As such, they are considered informal publications. The material presented in Administrative Reports may later be published in the formal scientific literature after more rigorous verification, editing, and peer review. Other publications are free to cite Administrative Reports as they wish provided the informal nature of the contents is clearly indicated and proper credit is given to the author(s). Administrative Reports may be cited as follows: Lozada-Misa P., B. D. Schumacher, and B. Vargas-Ángel. 2017. Analysis of benthic survey images via CoralNet: a summary of standard operating procedures and guidelines. Pacific Islands Fish. Sci. Cent., Natl. Mar. Fish. Serv., NOAA, Honolulu, HI 96818-5007. Pacific Islands Fish. Sci. Cent. Admin. Rep. H-17-02, 175 p. https://doi.org/V5/10.7289/V5/AR-PIFSC-H-17-02. __________________________ For further information direct inquiries to Chief, Scientific Information Services Pacific Islands Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration U.S. Department of Commerce 1845 Wasp Boulevard Building #176 Honolulu, Hawaiʻi 96818 Phone: 808-725-5331 Fax: 808-725-5532 Pacific Islands Fisheries Science Center Administrative Report H-17-02 https://doi.org/V5/10.7289/V5/AR-PIFSC-H-17-02 Analysis of Benthic Survey Images via CoralNet: a Summary of Standard Operating Procedures and Guidelines Paula Lozada-Misa Brett D. Schumacher Bernardo Vargas-Ángel Joint Institute for Marine and Atmospheric Research University of Hawaiʻi 1000 Pope Road Honolulu, Hawaiʻi 96822 January 2017 ii CONTENTS I. INTRODUCTION .................................................................................................................. 5 II. BACKGROUND ..................................................................................................................... 5 III. METHODS – BENTHIC IMAGE ANALYSIS STANDARD OPERATING PROCEDURES ............................................................................................................................. 2 III.A. CORALNET USER GUIDE............................................................................................... 2 III.A.1. SET UP YOUR CORALNET ACCOUNT ........................................................................... 3 III.A.2. ANALYST INTER-CALIBRATION PROCESS .................................................................... 4 III.A.3. ANALYZING IMAGES .................................................................................................... 8 III.A.3.1. ANALYZING RAPID ECOLOGICAL ASSESSMENT (REA) IMAGES ............................ 8 III.A.3.2. ANALYZING TOWED-DIVER SURVEY (TDS) IMAGES .......................................... 13 III.A.4. IMAGE ANALYSIS GUIDELINES .................................................................................. 18 III.A.5. TRACKING YOUR PROGRESS ....................................................................................... 21 III.B. SETTING UP A NEW SOURCE IN CORALNET .................................................................. 22 III.B.1. CREATING A NEW SOURCE ......................................................................................... 22 III.B.2. CREATING A LABELSET .............................................................................................. 24 III. C. UPLOADING IMAGES TO CORALNET ............................................................................ 28 III.C.1. FORMATTING IMAGE FILENAMES ............................................................................... 28 III.C.2. CONSOLIDATING IMAGE FILES ................................................................................... 29 III.C.3. IMAGE COLOR-CORRECTION VIA PICASA .................................................................. 30 III.C.4. UPLOADING IMAGE FILES AND ANNOTATIONS ........................................................... 34 IV. GUIDES ................................................................................................................................. 41 IV.A. BENTHIC IMAGE ANALYSIS – CLASSIFICATION GUIDE (TIER 3B) FOR RAPID ECOLOGICAL ASSESSMENT (REA) IMAGES ............................................................................ 41 IV. A.1. CORAL ...................................................................................................................... 43 IV.A.1.A. CORAL GENERA ................................................................................................. 45 IV.A.1.B. CORAL FUNCTIONAL GROUPS ............................................................................ 91 IV.A.2 SOFT CORAL ............................................................................................................... 99 IV.A.3. INVERTEBRATE ........................................................................................................ 100 IV.A.3.A. PORIFERA ......................................................................................................... 100 IV.A.3.B. CNIDARIA ......................................................................................................... 101 IV.A.3.C. MOLLUSCA ....................................................................................................... 103 IV.A.3.D. BRYOZOA/ECOPROCTA .................................................................................... 104 IV.A.3.E. CHORDATA ....................................................................................................... 104 IV.A.3.F. OTHER OR UNIDENTIFIABLE SESSILE INVERTEBRATES ..................................... 105 IV.A.4. MACROALGAE ......................................................................................................... 105 IV.A.4.A. FLESHY MACROALGAE ..................................................................................... 107 iii IV.A.4.B. OTHER MACROALGAE GROUPS ......................................................................... 119 IV.A.5. CRUSTOSE CORALLINE ALGAE ................................................................................ 124 IV.A.6. TURF ALGAE ............................................................................................................ 125 IV.A.7. SEDIMENT ................................................................................................................ 128 IV.A.8. MOBILE FAUNA ....................................................................................................... 129 IV.A.9. UNCLASSIFIED ......................................................................................................... 130 IV.A.10. TAPE/WAND .......................................................................................................... 131 IV.B. BENTHIC IMAGE ANALYSIS – CLASSIFICATION GUIDE (TIER 2) FOR TOWED-DIVER SURVEY (TDS) IMAGES .......................................................................................................... 132 IV.B.1. CORAL FUNCTIONAL GROUPS .................................................................................. 132 IV.B.2. SOFT CORAL ............................................................................................................ 141 IV.B.3. INVERTEBRATE ........................................................................................................ 142 IV.B.3.A. PORIFERA ......................................................................................................... 142 IV.B.3.B. CNIDARIA ......................................................................................................... 144 IV.B.3.C. MOLLUSCA ....................................................................................................... 146 IV.B.3.D. BRYOZOA/ECOPROCTA ..................................................................................... 147 IV.B.3.E. CHORDATA ....................................................................................................... 148 IV.B.3.F. OTHER OR UNIDENTIFIABLE SESSILE INVERTEBRATES ....................................... 148 IV.B.4. MACROALGAE ......................................................................................................... 149 IV.B.5. TURF ALGAE ............................................................................................................ 155 IV.B.6. SEDIMENT ................................................................................................................ 158 IV.B.7. MOBILE FAUNA ....................................................................................................... 159 IV.B.8. UNCLASSIFIED ......................................................................................................... 160 IV.B.9. TAPE/WAND ............................................................................................................ 161 IV.C. BENTHIC CLASSIFICATION TIERS – MAPPING