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                        "description": "JNCC requires the analysis of seabed imagery (stills and video) collected on the DY200 survey from the drop-down camera and Autonomous Underwater Vehicle (AUV). As the survey has not been completed yet, estimates of still image numbers and video length have been provided. These numbers may be subject to change after the survey and will be discussed with the relevant contractor.\nTable 2 Estimated number of stills and video data to be analysed from DY200.\nData type\tQuantity\nDrop camera video\t50 hours video\nDrop camera stills\t5,000 images\nAUV stills\t1,000 images\nThe following will be supplied to the successful contractor:\n•\tAccess to BIIGLE project with all stills, video and label trees. \no\tPlease email the contacts for technical information (see page 1) if you would like to be added as a guest to the BIIGLE project to review the imagery.\n•\tEpibiota Quality Assurance Framework Proforma spreadsheets\n4.\tProject Objectives\n1.\tAnalysis of stills and video taken with the drop-camera system\n2.\tFiltering, processing and analysis of a subset of AUV imagery\n3.\tProvide substrate and taxonomic image reference collections for each substrate type and taxon identified from imagery.\n4.\tProduce a final analysis report including, at a minimum, sections detailing the methodology, results , and details of all QA work undertaken with any remedial action deemed necessary. The report should be no longer than 10,000 words including all tables and appendices and be provided electronically via email as a Microsoft Word document.\n5.\tProduce a report comparing the ability of the AUV and the drop camera to identify the following deep-sea features (if present in the AUV data) and make recommendations on the most appropriate survey technique for these features.\no\tCoral gardens\no\tSeapen and burrowing megafauna\no\tDeep Sea Sponge aggregations (if present in the data collected)\n6.\tCreate a subset of stills annotated in a way suitable to act as training data for artificial intelligence model training as described below\nThe contractor must\n•\tUndertake the analysis as set out below and adhering to the NMBAQC Epibiota interpretation guidelines (Turner et al, 2016). Please note these guidelines are currently being updated by JNCC - the contractor must check with JNCC if the updated guidelines are available when the contract starts.\n•\tUse BIIGLE to annotate video and stills as described below. Alternative image annotation software may be used subject to agreement with the project officer.\n•\tEnsure that stills and video references used in analysis outputs are identical to those used in the naming of the original media to enable future reconciliation between data and media. If identical naming is not possible, a suitable alternative should be sought with JNCC.\nSome information, where specified, may be recorded directly into the proformas provided. The majority will be recorded first into BIIGLE and then used to populate the proforma. No analysis additional to what is described in this document is required. Any deviation from this methodology should be approved in writing by the project officer.\n4.1.\tAnalysis of video data from drop-camera \nVideo should be analysed in BIIGLE using the label trees shown in Table 2. A high-level review should be conducted as described in section 2.1 of Turner et al (2016). Annotations can be added to videos as either tier 1 or tier 2 annotations depending on the label tree used. More details on the video annotation tiers and how they should be applied are provided in Appendix A.\nVideo will be analysed to extract the following information (all information should be recorded using the provided BIIGLE label trees, unless specified otherwise):\n1.\tVideo should be segmented into areas of continuous broadscale seabed habitat type (detailed in step 2) greater than or equal to 5 m along transect distance; JNCC will provide positional information for this purpose. The segment label tree should be used to delineate these segments and labels from other trees should be attached to each segment using the \"add label\" tool in BIIGLE.\n2.\tThe Marine Habitat Classification of Britain and Ireland (v 22.04) will be used, and a new segment should be started if the habitat classification changes.   \n3.\tEach segment will be assigned image quality scores using labels from the following two label trees. Further analysis of video segments will be dependent on the image quality score. For example, if a segment is given a score of zero, no further analysis should be carried out for that segment.\na.\tNMBAQC image quality, a summary of these scores is shown in Table 3 and described in more detail in section 2.1 of Turner et al (2016).\nb.\tJNCC image quality, a summary of these labels is shown in Table 4.\n4.\tIdentify evidence of anthropogenic impacts on the seabed:\na.\tUse the litter label tree to record the presence of litter using the categories listed in Annex 5.1 of the Joint Research Centres Guidance on Monitoring of Marine Litter in European Seas6. \nb.\tUse the Anthropogenic label tree to annotate trawl marks or anthropogenic impacts other than litter. This will not be a complete label tree and new labels may need to be added to the label tree.\n5.\tUse the biotope label tree to assign biotopes, up to level 6 of the Marine habitat classification of Britain and Ireland hierarchy and in accordance with Parry (2019)7.\nTable 3 Label trees for video annotation and the annotation type which should be used for each label tree\nVideo analysis label tree\tVideo annotation type\nSegment\tTier 1\nMarine habitat classification of Britain and Ireland (v 22.04)\tTier 1\nJNCC image quality\tTier 1\nNMBAQC image quality\tTier 1\nBiotope\tTier 1\nCoral Gardens (Henry and Roberts, 2014a)\nTier 1\nSeapen and Burrowing Megafauna \n(please note the definition of this FOCI currently being updated by JNCC - see Appendix B)\tTier 1\nDeep Sea Sponge Aggregations (Henry and Roberts, 2014b)\nTier 1\nCoral Reef (if present)\tTier 1\nBurrows\tTier 1\nLitter\tTier 2\nAnthropogenic\tTier 2\nTable 4 Summary of NMBAQC image quality categories (Turner et al., 2016)\nTable 5 JNCC image quality categories\n•\tImagery quality level\t•\tDescription\n•\tFauna\t•\tMost fauna can be identified (e.g. including smaller taxa such as brittlestars etc.)\n•\tConspicuous fauna\t•\tLarge and conspicuous fauna can be identified (e.g. sponges, soft corals etc.)\n•\tSubstrate\t•\tThe substrate type can be identified, but the fauna cannot (e.g. the water column is obscured / the camera is too high off the seabed)\n•\tZero\t•\tNo visibility of the seabed, substrate cannot be identified.\n4.2.\tAnalysis of stills data from drop-camera and AUV\nStills should be analysed in BIIGLE using the label trees used. Some tier 1 labels may be added directly into the proforma (see below). More details on the still annotation types and how they should be applied are provided in Appendix A.\nTable 6 Label trees for stills annotation and the annotation type which should be used for each label tree\nStills analysis label tree\tStills annotation type\nNMBAQC image quality\tTier 1\nJNCC image quality\tTier 1\nSubstrate\tTier 1\nBiota\tTier 2\nLaser points\tTier 2\nLitter\tTier 2\nAnthropogenic\tTier 2\nStills will be analysed to extract the following information:\n1.\tEach still will be assigned image quality scores using labels from the following two label trees. Further analysis of the still image will be dependent on the image quality score. For example, if a still image is given a score of 'very poor' and 'substrate', no taxonomic identification should be carried out for that still image.\na.\tNMBAQC image quality, a summary of these scores is shown in Table 3 and described in more detail in section 2.1 of Turner et al 2016.\nb.\tJNCC image quality, a summary of these labels is shown in Table 4.\n2.\tIdentification and enumeration of epifauna, JNCC will provide a reference collection built from images previously taken in these sites. Annotations made using the Biota label tree. For each still image being analysed, identify, and quantify all8:\na.\tSolitary and/or erect epifaunal species present.\nb.\tBioturbation traces using counts (achieved by using the point annotation tool within BIIGLE). \nc.\tColonial and/or encrusting epifaunal species present as far as possible (using percentage cover (achieved by using the polygon, magic wand, or brush tools within BIIGLE).\n3.\tRecord substrate type and Faunal Turf cover to nearest 10% directly to proforma. \n4.\tUse laser points label tree to annotate lasers and calculate image area in BIIGLE. Analysts are not to use the automated laser detection tool in BIIGLE.\n5.\tIdentify evidence of anthropogenic impacts on the seabed: \na.\tUse the litter label tree to record the presence of litter using the categories listed in Annex 5.1 of the Joint Research Centres Guidance on Monitoring of Marine Litter in European Seas6\nb.\tUse the Anthropogenic label tree to annotate trawl marks or anthropogenic impacts other than litter. Note, new labels may need to be added to the label tree.\n6.\t          4.3.\tDeveloping training data for artificial intelligence\nIn addition to providing costs for the analysis described above, please provide quotes for the following preparation of 100 stills from the drop-camera in BIIGLE to form a suitable training dataset for Artificial Intelligence models:\n1.\tStills will be re-annotated using a bounding box. Images of image quality zero (NMBAQC equivalent) should be excluded:\na.\tAll points and polygons must be converted into a rectangle suitable for use in an AI model\nb.\tExample box annotations for fauna annotated with a point will be provided to the successful contractor to enable an average box size (in pixels) to be estimated\n2.\tJNCC will provide 100 images randomly selected from across the dataset and from varying time points in a transect . \n3.\tRe-annotated images will be stored in a separate BIIGLE volume within the 2023 PBR survey project.",
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                    "title": "The Canyons MCZ DY200 drop camera & AUV data analysis",
                    "description": "JNCC requires the analysis of seabed imagery (stills and video) collected on the DY200 survey from the drop-down camera and Autonomous Underwater Vehicle (AUV). As the survey has not been completed yet, estimates of still image numbers and video length have been provided. These numbers may be subject to change after the survey and will be discussed with the relevant contractor.\nTable 2 Estimated number of stills and video data to be analysed from DY200.\nData type\tQuantity\nDrop camera video\t50 hours video\nDrop camera stills\t5,000 images\nAUV stills\t1,000 images\nThe following will be supplied to the successful contractor:\n•\tAccess to BIIGLE project with all stills, video and label trees. \no\tPlease email the contacts for technical information (see page 1) if you would like to be added as a guest to the BIIGLE project to review the imagery.\n•\tEpibiota Quality Assurance Framework Proforma spreadsheets\n4.\tProject Objectives\n1.\tAnalysis of stills and video taken with the drop-camera system\n2.\tFiltering, processing and analysis of a subset of AUV imagery\n3.\tProvide substrate and taxonomic image reference collections for each substrate type and taxon identified from imagery.\n4.\tProduce a final analysis report including, at a minimum, sections detailing the methodology, results , and details of all QA work undertaken with any remedial action deemed necessary. 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Please note these guidelines are currently being updated by JNCC - the contractor must check with JNCC if the updated guidelines are available when the contract starts.\n•\tUse BIIGLE to annotate video and stills as described below. Alternative image annotation software may be used subject to agreement with the project officer.\n•\tEnsure that stills and video references used in analysis outputs are identical to those used in the naming of the original media to enable future reconciliation between data and media. If identical naming is not possible, a suitable alternative should be sought with JNCC.\nSome information, where specified, may be recorded directly into the proformas provided. The majority will be recorded first into BIIGLE and then used to populate the proforma. No analysis additional to what is described in this document is required. Any deviation from this methodology should be approved in writing by the project officer.\n4.1.\tAnalysis of video data from drop-camera \nVideo should be analysed in BIIGLE using the label trees shown in Table 2. A high-level review should be conducted as described in section 2.1 of Turner et al (2016). Annotations can be added to videos as either tier 1 or tier 2 annotations depending on the label tree used. More details on the video annotation tiers and how they should be applied are provided in Appendix A.\nVideo will be analysed to extract the following information (all information should be recorded using the provided BIIGLE label trees, unless specified otherwise):\n1.\tVideo should be segmented into areas of continuous broadscale seabed habitat type (detailed in step 2) greater than or equal to 5 m along transect distance; JNCC will provide positional information for this purpose. The segment label tree should be used to delineate these segments and labels from other trees should be attached to each segment using the \"add label\" tool in BIIGLE.\n2.\tThe Marine Habitat Classification of Britain and Ireland (v 22.04) will be used, and a new segment should be started if the habitat classification changes.   \n3.\tEach segment will be assigned image quality scores using labels from the following two label trees. Further analysis of video segments will be dependent on the image quality score. For example, if a segment is given a score of zero, no further analysis should be carried out for that segment.\na.\tNMBAQC image quality, a summary of these scores is shown in Table 3 and described in more detail in section 2.1 of Turner et al (2016).\nb.\tJNCC image quality, a summary of these labels is shown in Table 4.\n4.\tIdentify evidence of anthropogenic impacts on the seabed:\na.\tUse the litter label tree to record the presence of litter using the categories listed in Annex 5.1 of the Joint Research Centres Guidance on Monitoring of Marine Litter in European Seas6. \nb.\tUse the Anthropogenic label tree to annotate trawl marks or anthropogenic impacts other than litter. This will not be a complete label tree and new labels may need to be added to the label tree.\n5.\tUse the biotope label tree to assign biotopes, up to level 6 of the Marine habitat classification of Britain and Ireland hierarchy and in accordance with Parry (2019)7.\nTable 3 Label trees for video annotation and the annotation type which should be used for each label tree\nVideo analysis label tree\tVideo annotation type\nSegment\tTier 1\nMarine habitat classification of Britain and Ireland (v 22.04)\tTier 1\nJNCC image quality\tTier 1\nNMBAQC image quality\tTier 1\nBiotope\tTier 1\nCoral Gardens (Henry and Roberts, 2014a)\nTier 1\nSeapen and Burrowing Megafauna \n(please note the definition of this FOCI currently being updated by JNCC - see Appendix B)\tTier 1\nDeep Sea Sponge Aggregations (Henry and Roberts, 2014b)\nTier 1\nCoral Reef (if present)\tTier 1\nBurrows\tTier 1\nLitter\tTier 2\nAnthropogenic\tTier 2\nTable 4 Summary of NMBAQC image quality categories (Turner et al., 2016)\nTable 5 JNCC image quality categories\n•\tImagery quality level\t•\tDescription\n•\tFauna\t•\tMost fauna can be identified (e.g. including smaller taxa such as brittlestars etc.)\n•\tConspicuous fauna\t•\tLarge and conspicuous fauna can be identified (e.g. sponges, soft corals etc.)\n•\tSubstrate\t•\tThe substrate type can be identified, but the fauna cannot (e.g. the water column is obscured / the camera is too high off the seabed)\n•\tZero\t•\tNo visibility of the seabed, substrate cannot be identified.\n4.2.\tAnalysis of stills data from drop-camera and AUV\nStills should be analysed in BIIGLE using the label trees used. Some tier 1 labels may be added directly into the proforma (see below). More details on the still annotation types and how they should be applied are provided in Appendix A.\nTable 6 Label trees for stills annotation and the annotation type which should be used for each label tree\nStills analysis label tree\tStills annotation type\nNMBAQC image quality\tTier 1\nJNCC image quality\tTier 1\nSubstrate\tTier 1\nBiota\tTier 2\nLaser points\tTier 2\nLitter\tTier 2\nAnthropogenic\tTier 2\nStills will be analysed to extract the following information:\n1.\tEach still will be assigned image quality scores using labels from the following two label trees. Further analysis of the still image will be dependent on the image quality score. For example, if a still image is given a score of 'very poor' and 'substrate', no taxonomic identification should be carried out for that still image.\na.\tNMBAQC image quality, a summary of these scores is shown in Table 3 and described in more detail in section 2.1 of Turner et al 2016.\nb.\tJNCC image quality, a summary of these labels is shown in Table 4.\n2.\tIdentification and enumeration of epifauna, JNCC will provide a reference collection built from images previously taken in these sites. Annotations made using the Biota label tree. For each still image being analysed, identify, and quantify all8:\na.\tSolitary and/or erect epifaunal species present.\nb.\tBioturbation traces using counts (achieved by using the point annotation tool within BIIGLE). \nc.\tColonial and/or encrusting epifaunal species present as far as possible (using percentage cover (achieved by using the polygon, magic wand, or brush tools within BIIGLE).\n3.\tRecord substrate type and Faunal Turf cover to nearest 10% directly to proforma. \n4.\tUse laser points label tree to annotate lasers and calculate image area in BIIGLE. 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These numbers may be subject to change after the survey and will be discussed with the relevant contractor.\nTable 2 Estimated number of stills and video data to be analysed from DY200.\nData type\tQuantity\nDrop camera video\t50 hours video\nDrop camera stills\t5,000 images\nAUV stills\t1,000 images\nThe following will be supplied to the successful contractor:\n•\tAccess to BIIGLE project with all stills, video and label trees. \no\tPlease email the contacts for technical information (see page 1) if you would like to be added as a guest to the BIIGLE project to review the imagery.\n•\tEpibiota Quality Assurance Framework Proforma spreadsheets\n4.\tProject Objectives\n1.\tAnalysis of stills and video taken with the drop-camera system\n2.\tFiltering, processing and analysis of a subset of AUV imagery\n3.\tProvide substrate and taxonomic image reference collections for each substrate type and taxon identified from imagery.\n4.\tProduce a final analysis report including, at a minimum, sections detailing the methodology, results , and details of all QA work undertaken with any remedial action deemed necessary. The report should be no longer than 10,000 words including all tables and appendices and be provided electronically via email as a Microsoft Word document.\n5.\tProduce a report comparing the ability of the AUV and the drop camera to identify the following deep-sea features (if present in the AUV data) and make recommendations on the most appropriate survey technique for these features.\no\tCoral gardens\no\tSeapen and burrowing megafauna\no\tDeep Sea Sponge aggregations (if present in the data collected)\n6.\tCreate a subset of stills annotated in a way suitable to act as training data for artificial intelligence model training as described below\nThe contractor must\n•\tUndertake the analysis as set out below and adhering to the NMBAQC Epibiota interpretation guidelines (Turner et al, 2016). Please note these guidelines are currently being updated by JNCC - the contractor must check with JNCC if the updated guidelines are available when the contract starts.\n•\tUse BIIGLE to annotate video and stills as described below. Alternative image annotation software may be used subject to agreement with the project officer.\n•\tEnsure that stills and video references used in analysis outputs are identical to those used in the naming of the original media to enable future reconciliation between data and media. If identical naming is not possible, a suitable alternative should be sought with JNCC.\nSome information, where specified, may be recorded directly into the proformas provided. The majority will be recorded first into BIIGLE and then used to populate the proforma. No analysis additional to what is described in this document is required. Any deviation from this methodology should be approved in writing by the project officer.\n4.1.\tAnalysis of video data from drop-camera \nVideo should be analysed in BIIGLE using the label trees shown in Table 2. A high-level review should be conducted as described in section 2.1 of Turner et al (2016). Annotations can be added to videos as either tier 1 or tier 2 annotations depending on the label tree used. More details on the video annotation tiers and how they should be applied are provided in Appendix A.\nVideo will be analysed to extract the following information (all information should be recorded using the provided BIIGLE label trees, unless specified otherwise):\n1.\tVideo should be segmented into areas of continuous broadscale seabed habitat type (detailed in step 2) greater than or equal to 5 m along transect distance; JNCC will provide positional information for this purpose. The segment label tree should be used to delineate these segments and labels from other trees should be attached to each segment using the \"add label\" tool in BIIGLE.\n2.\tThe Marine Habitat Classification of Britain and Ireland (v 22.04) will be used, and a new segment should be started if the habitat classification changes.   \n3.\tEach segment will be assigned image quality scores using labels from the following two label trees. Further analysis of video segments will be dependent on the image quality score. For example, if a segment is given a score of zero, no further analysis should be carried out for that segment.\na.\tNMBAQC image quality, a summary of these scores is shown in Table 3 and described in more detail in section 2.1 of Turner et al (2016).\nb.\tJNCC image quality, a summary of these labels is shown in Table 4.\n4.\tIdentify evidence of anthropogenic impacts on the seabed:\na.\tUse the litter label tree to record the presence of litter using the categories listed in Annex 5.1 of the Joint Research Centres Guidance on Monitoring of Marine Litter in European Seas6. \nb.\tUse the Anthropogenic label tree to annotate trawl marks or anthropogenic impacts other than litter. This will not be a complete label tree and new labels may need to be added to the label tree.\n5.\tUse the biotope label tree to assign biotopes, up to level 6 of the Marine habitat classification of Britain and Ireland hierarchy and in accordance with Parry (2019)7.\nTable 3 Label trees for video annotation and the annotation type which should be used for each label tree\nVideo analysis label tree\tVideo annotation type\nSegment\tTier 1\nMarine habitat classification of Britain and Ireland (v 22.04)\tTier 1\nJNCC image quality\tTier 1\nNMBAQC image quality\tTier 1\nBiotope\tTier 1\nCoral Gardens (Henry and Roberts, 2014a)\nTier 1\nSeapen and Burrowing Megafauna \n(please note the definition of this FOCI currently being updated by JNCC - see Appendix B)\tTier 1\nDeep Sea Sponge Aggregations (Henry and Roberts, 2014b)\nTier 1\nCoral Reef (if present)\tTier 1\nBurrows\tTier 1\nLitter\tTier 2\nAnthropogenic\tTier 2\nTable 4 Summary of NMBAQC image quality categories (Turner et al., 2016)\nTable 5 JNCC image quality categories\n•\tImagery quality level\t•\tDescription\n•\tFauna\t•\tMost fauna can be identified (e.g. including smaller taxa such as brittlestars etc.)\n•\tConspicuous fauna\t•\tLarge and conspicuous fauna can be identified (e.g. sponges, soft corals etc.)\n•\tSubstrate\t•\tThe substrate type can be identified, but the fauna cannot (e.g. the water column is obscured / the camera is too high off the seabed)\n•\tZero\t•\tNo visibility of the seabed, substrate cannot be identified.\n4.2.\tAnalysis of stills data from drop-camera and AUV\nStills should be analysed in BIIGLE using the label trees used. Some tier 1 labels may be added directly into the proforma (see below). More details on the still annotation types and how they should be applied are provided in Appendix A.\nTable 6 Label trees for stills annotation and the annotation type which should be used for each label tree\nStills analysis label tree\tStills annotation type\nNMBAQC image quality\tTier 1\nJNCC image quality\tTier 1\nSubstrate\tTier 1\nBiota\tTier 2\nLaser points\tTier 2\nLitter\tTier 2\nAnthropogenic\tTier 2\nStills will be analysed to extract the following information:\n1.\tEach still will be assigned image quality scores using labels from the following two label trees. Further analysis of the still image will be dependent on the image quality score. For example, if a still image is given a score of 'very poor' and 'substrate', no taxonomic identification should be carried out for that still image.\na.\tNMBAQC image quality, a summary of these scores is shown in Table 3 and described in more detail in section 2.1 of Turner et al 2016.\nb.\tJNCC image quality, a summary of these labels is shown in Table 4.\n2.\tIdentification and enumeration of epifauna, JNCC will provide a reference collection built from images previously taken in these sites. Annotations made using the Biota label tree. For each still image being analysed, identify, and quantify all8:\na.\tSolitary and/or erect epifaunal species present.\nb.\tBioturbation traces using counts (achieved by using the point annotation tool within BIIGLE). \nc.\tColonial and/or encrusting epifaunal species present as far as possible (using percentage cover (achieved by using the polygon, magic wand, or brush tools within BIIGLE).\n3.\tRecord substrate type and Faunal Turf cover to nearest 10% directly to proforma. \n4.\tUse laser points label tree to annotate lasers and calculate image area in BIIGLE. Analysts are not to use the automated laser detection tool in BIIGLE.\n5.\tIdentify evidence of anthropogenic impacts on the seabed: \na.\tUse the litter label tree to record the presence of litter using the categories listed in Annex 5.1 of the Joint Research Centres Guidance on Monitoring of Marine Litter in European Seas6\nb.\tUse the Anthropogenic label tree to annotate trawl marks or anthropogenic impacts other than litter. Note, new labels may need to be added to the label tree.\n6.\t          4.3.\tDeveloping training data for artificial intelligence\nIn addition to providing costs for the analysis described above, please provide quotes for the following preparation of 100 stills from the drop-camera in BIIGLE to form a suitable training dataset for Artificial Intelligence models:\n1.\tStills will be re-annotated using a bounding box. Images of image quality zero (NMBAQC equivalent) should be excluded:\na.\tAll points and polygons must be converted into a rectangle suitable for use in an AI model\nb.\tExample box annotations for fauna annotated with a point will be provided to the successful contractor to enable an average box size (in pixels) to be estimated\n2.\tJNCC will provide 100 images randomly selected from across the dataset and from varying time points in a transect . \n3.\tRe-annotated images will be stored in a separate BIIGLE volume within the 2023 PBR survey project."
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