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Forest Protection Survey Program
Survey Guideline - DigiKam Images (V3)
Acknowledgements
Louise Durkin and Jenny Nelson of the Arthur Rylah Institute for Environmental Research
Author
Jemma Cripps, Arthur Rylah Institute for Environmental Research
Photo credit
Cover photo: Arthur Rylah Institute for Environmental Research 2018
© The State of Victoria Department of Environment, Land, Water and Planning 2018
This work is licensed under a Creative Commons Attribution 4.0 International licence. You are free to re-use the work under that licence, on the condition that you credit the State of Victoria as author. The licence does not apply to any images, photographs or branding, including the Victorian Coat of Arms, the Victorian Government logo and the
Department of Environment, Land, Water and Planning (DELWP) logo. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/
Disclaimer
This publication may be of assistance to you but the State of Victoria and its employees do not guarantee that the publication is without flaw of any kind or is wholly appropriate for your particular purposes and therefore disclaims all liability for any error, loss or other consequence which may arise from you relying on any information in this publication.
Accessibility
If you would like to receive this publication in an alternative format, please telephone the
DELWP Customer Service Centre on 136186, email [email protected],
or via the National Relay Service on 133 677 www.relayservice.com.au. This document is
also available on the internet at www.delwp.vic.gov.au.
1. Protocol for tagging species ID in remote camera images using digiKam software ............................................................................................................................. 2
1.1 Purpose ...................................................................................................................................................... 2
1.2 Setting up digiKam for the first time ....................................................................................................... 2
1.3 Metadata tag structure and tagging images ........................................................................................... 4
1.4 Review your work .................................................................................................................................... 10
1.5 Expert review of ‘XXX’ tags .................................................................................................................... 12
1.6 List of species tags ................................................................................................................................. 12
Contents
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1. Protocol for tagging species ID in remote camera images using digiKam software
1.1 Purpose
A method is needed to consistently and efficiently process remote camera data collected during the Forest
Protection survey program (FPSP). Species data will be used to improve our knowledge of detection
probabilities and will be analysed by ARI using the CamtrapR package in R.
This document describes the method using digiKam as the software for image tagging. DigiKam is
compatible with the camptrapR package. Metadata tags can be assigned to images in image management
software such as digiKam. They are saved in the image metadata automatically. Metadata tagging can be
used to assign custom tags to images, e.g. species ID, number of individuals on images.
1.2 Setting up digiKam for the first time
Download digiKam at https://www.digikam.org/download/
Install digiKam
digiKam needs to write metadata tags into image metadata, not into .xmp sidecar files. Its behaviour can be configured. Here’s how to set up digiKam:
If installing for the first time, it will ask you to make a few settings when you first start the program. When asked “Configure Metadata Storage to Files”, set “Add Information to Files” instead of the default “Do Nothing”.
If digiKam was installed already, go to “Settings”, then “Configure digiKam”. There, select “Metadata” on the left and, in the tab “Behaviour”, make sure that “Image tags” is checked in the box titled “Write This Information to the Metadata”.
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Below, in the box “Reading and Writing Metadata”, make sure that both “Read from sidecar files” and “Write
to sidecar files” are unchecked.
Also in “Settings”, “Configure digiKam” – make sure your Collections Settings are set to the folder where
your images are stored. Click on “Collections” on the left, and then “Add Collection” to “Local
Collections”.
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1.3 Metadata tag structure and tagging images
Before assigning metadata tags, users need to set up a hierarchical tag structure for the tagging to be
compatible with camtrapR. This structure is customisable and can be expanded as needed. In digiKam, this
is done in the Tag Manager. Here’s some examples:
• Species
o SpeciesA
o SpeciesB
• Individual
o Two individuals
o Three individuals
o Four or more individuals
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Make sure the image named “PHS_species_tags.jpg” (provided by DELWP) is in the same folder path
as the photos you are planning to tag.
NOTE: This image is tagged with all the possible species tags and already structured in a hierarchical
way. Tags will therefore be automatically recognised in Tag Manager. This will ensure consistency in tag
use between contractors tagging images.
For a full list of species tags for the FPSP, see Table 1 below and Appendix 1.
Table 1: explanations for use of method tags
Tag Explanation
AAA
Images taken during the camera setup.
IDX
There is an animal visible, but it’s not possible to identify it
(e.g. you can only see a furry blur or a tail).
These images will be excluded from further analysis.
NIL There is no animal present (e.g. wind trigger).
These images will be excluded from further analysis.
XXX This is an identifiable animal, and I think it’s a particular species, but I’m not 100% confident.
These images are to be reviewed by one or more experts before analysis and either
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confirmed (i.e. XXX tag removed) or changed to IDX.
An XXX tag should always be accompanied by a species tag, never on its own:
ZZZ Images taken when the camera was retrieved.
In the Album pane (left), select a single camera deployment folder at a time. (Note: if you select a higher-
order folder, you’ll see all the related subfolders as thumbnails).
Make sure that the “Captions” tab is selected in the right pane. Select the tab named “Tags”.
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In the thumbnail pane (centre), click on the first image. Now you can use the arrow keys (on the keyboard) to
efficiently move through the images in sequence.
Start by applying the ‘camera deployment’ tag (i.e. when the camera was set up initially), which is ‘AAA’, to
the first images. Click on the first thumbnail.
Hold down the ‘Shift’ key on your keyboard and click on the last photo corresponding to deployment. This
should highlight all the relevant images (12 in the case below):
In the tag pane, tick the ‘AAA’ tag:
After a short delay, you should see that the tags are applied to the selected thumbnails.
Continue to move through the images using the arrow keys, adding species tags to each image, or cluster of
images (using ‘Shift’ to batch process).
Use the search function at the bottom of the tag list to find the species tag you are looking for using
keywords e.g. “red” – see example below.
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Multiple tags can be applied to a single image, either if more than one species is visible, more than two
individuals are present, or using the ‘XXX’ tag to denote an ID that needs confirmation.
Tags should be applied consistently to all images from a single trigger event. Using camera settings
as per the FPSP guidelines, this means tagging images in batches of three/five. For example, if the first
image from a trigger is clearly a Mountain Brushtail, the next image only shows the animal leaving camera
and couldn’t be identified to species based on that image alone, and the next image is empty, tag all three
images as ‘MBP’ (not ‘MBP’, ‘IDX’, and ’NIL’ in that order).
All images should be tagged with at least one tag, regardless of what’s visible or not.
If you make a mistake, just select the images and untick the wrong tag, then tick the correct one. Then click
Apply.
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If an animal is present over a sequence of several consecutive trigger events, and the species ID can only be
distinguished in some photos or some trigger events, but you can confidently infer the species ID across the
whole series of photos, then tag the whole series with the species ID.
1.4 Review your work
After completing tagging of all relevant deployments, search all folders for untagged images.
In the toolbar on the right side of the screen, click on the tab called Filters.
Tick the box at the bottom labelled Images without tags. This will select any images that have been missed in
the tagging process.
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Review your own ‘XXX’ tags. This time, use the Search tab on the toolbar on the left-hand side of the screen.
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Type in the keyword “XXX” to find all images tagged with this label.
Review these images and make sure each ‘XXX’ tag also has a species tag (as per Table 1 guidance).
Review these decisions if required (remove the ‘XXX’ if you’re now confident of the species ID) or keep them
for later expert review.
1.5 Expert review of ‘XXX’ tags
This should be performed by a person with appropriate ID skills and taxonomic expertise, before final results
are uploaded or exported for storage and analysis.
Filter to view all ‘XXX’ tags as per the process above.
Review each image and either
(a) remove the ‘XXX’ tag to confirm the current species ID, or
(b) change to another species and remove the ‘XXX’ tag, or
(c) remove both the ‘XXX’ and species tag,and replace with ‘IDX’.
Once done, there should be no remaining ‘XXX’ tags, and no more visible thumbnails.
1.6 List of species tags
VBA taxon ID Common name Scientific Name Tag
11028 Agile Antechinus Antechinus agilis Agile Antechinus
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VBA taxon ID Common name Scientific Name Tag
11817 Antechinus Antechinus Antechinus
10281 Australian King-Parrot Alisterus scapularis Australian King-Parrot
10705 Australian Magpie Gymnorhina tibicen Australian Magpie
10317 Australian Owlet-nightjar Aegotheles cristatus Australian Owlet-nightjar
10202 Australian Wood Duck Chenonetta jubata Australian Wood Duck
61801 Bandicoots Bandicoot Bandicoots
10246 Barking Owl Ninox connivens connivens Barking Owl
10779 Bassian Thrush Zoothera lunulata Bassian Thrush
10650 Beautiful Firetail Stagonopleura bella Beautiful Firetail
10633 Bell Miner Manorina melanophrys Bell Miner
NA Bird species Bird spp.
11408 Black Rat Rattus rattus Black Rat
11242 Black-tailed Wallaby Wallabia bicolor Black-tailed Wallaby
11438 Broad-toothed Rat Mastacomys fuscus mordicus Broad-toothed Rat
11409 Brown Rat Rattus norvegicus Brown Rat
10475 Brown Thornbill Acanthiza pusilla Brown Thornbill
60555 Brown Treecreeper (south-eastern ssp.) Climacteris picumnus victoriae
Brown Treecreeper (south-eastern ssp.)
10339 Brush Cuckoo Cacomantis variolosus Brush Cuckoo
11802 Brushtail Possums Trichosurus Brushtail Possums
11017 Brush-tailed Phascogale Phascogale tapoatafa Brush-tailed Phascogale
10484 Buff-rumped Thornbill Acanthiza reguloides Buff-rumped Thornbill
11395 Bush Rat Rattus fuscipes Bush Rat
11536 Cat Felis catus Cat
10991 Common Blackbird Turdus merula Common Blackbird
10034 Common Bronzewing Phaps chalcoptera Common Bronzewing
11113 Common Brush-tailed Possum Trichosurus vulpecula Common Brush-tailed Possum
11061 Common Dunnart Sminthopsis murina murina Common Dunnart
11129 Eastern Ring-tailed Possum Pseudocheirus peregrinus Eastern Ring-tailed Possum
10999 Common Starling Sturnus vulgaris Common Starling
11165 Common Wombat Vombatus ursinus Common Wombat
11518 Cattle (feral) Bos taurus Cattle (feral)
10630 Crescent Honeyeater Phylidonyris pyrrhoptera Crescent Honeyeater
10043 Crested Pigeon Ocyphaps lophotes Crested Pigeon
10416 Crested Shrike-tit Falcunculus frontatus Crested Shrike-tit
10282 Crimson Rosella Platycercus elegans Crimson Rosella
525834 Deer Cervidae Deer
10652 Diamond Firetail Stagonopleura guttata Diamond Firetail
61835 Dingo Canis lupus dingo/ Dingo
11836 Dog Canis lupus familiaris Dog
11033 Mainland Dusky Antechinus Antechinus mimetes Mainland Dusky Antechinus
10347 Eastern Koel Eudynamys orientalis Eastern Koel
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VBA taxon ID Common name Scientific Name Tag
11150 Eastern Pygmy-possum Cercartetus nanus Eastern Pygmy-possum
10288 Eastern Rosella Platycercus eximius Eastern Rosella
10591 Eastern Spinebill Acanthorhynchus tenuirostris Eastern Spinebill
10421 Eastern Whipbird Psophodes olivaceus Eastern Whipbird
10392 Eastern Yellow Robin Eopsaltria australis Eastern Yellow Robin
11003 Short-beaked Echidna Tachyglossus aculeatus Short-beaked Echidna
11265 Eastern Grey Kangaroo Macropus giganteus Eastern Grey Kangaroo
10001 Emu Dromaius novaehollandiae Emu
11511 European Hare Lepus europeaus European Hare
11510 European Rabbit Oryctolagus cuniculus European Rabbit
11523 Fallow Deer Cervus dama Fallow Deer
10338 Fan-tailed Cuckoo Cacomantis flabelliformis Fan-tailed Cuckoo
11147 Narrow-toed Feathertail Glider. Acrobates pygmaeus Narrow-toed Feathertail Glider
10382 Flame Robin Petroica phoenicea Flame Robin
528552 Red Fox Vulpes vulpes Fox
NA Frog spp. NA Frog spp.
10613 Fuscous Honeyeater Lichenostomus fuscus Fuscous Honeyeater
10273 Galah Eolophus roseicapilla Galah
10268 Gang-gang Cockatoo Callocephalon fimbriatum Gang-gang Cockatoo
11804 Gliders Petaurus Gliders
10265 Glossy Black-Cockatoo Calyptorhynchus lathami lathami Glossy Black-Cockatoo
12283 Lace Monitor Varanus varius Lace Monitor
11521 Goat (feral) Capra hircus Goat (feral)
10398 Golden Whistler Pachycephala pectoralis Golden Whistler
11133 Greater Glider Petauroides volans Greater Glider
10702 Grey Butcherbird Cracticus torquatus Grey Butcherbird
10697 Grey Currawong Strepera versicolor Grey Currawong
10236 Grey Falcon Falco hypoleucos Grey Falcon
10361 Grey Fantail Rhipidura albiscarpa Grey Fantail
10220 Grey Goshawk Accipiter novaehollandiae novaehollandiae Grey Goshawk
10408 Grey Shrike-thrush Colluricincla harmonica Grey Shrike-thrush
11525 Hog Deer Cervus porcinus Hog Deer
10385 Hooded Robin Melanodryas cucullata cucullata Hooded Robin
11512 Horse (feral) Equus caballus Horse (feral)
10342 Horsfield's Bronze-Cuckoo Chrysococcyx basalis Horsfields Bronze-Cuckoo
10995 House Sparrow Passer domesticus House Sparrow
10377 Jacky Winter Microeca fascinans Jacky Winter
11805 Kangaroo Macropus Kangaroo
11162 Koala Phascolarctos cinereus Koala
10322 Laughing Kookaburra Dacelo novaeguineae Laughing Kookaburra
10494 Large-billed Scrubwren Sericornis magnirostris Large-billed Scrubwren
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VBA taxon ID Common name Scientific Name Tag
11141 Leadbeater's Possum Gymnobelideus leadbeateri Leadbeater's Possum
10365 Leaden Flycatcher Myiagra rubecula Leaden Flycatcher
10605 Lewin's Honeyeater Meliphaga lewinii Lewins Honeyeater
10271 Little Corella Cacatua sanguinea Little Corella
10225 Little Eagle Hieraaetus morphnoides Little Eagle
10637 Little Wattlebird Anthochaera chrysoptera Little Wattlebird
11179 Long-footed Potoroo Potorous longipes Long footed Potoroo
10272 Long-billed Corella Cacatua tenuirostris Long-billed Corella
11097 Southern Long-nosed Bandicoot Perameles nasuta Southern Long-nosed Bandicoot
11175 Long-nosed Potoroo Potorous tridactylus tridactylus Long-nosed Potoroo
10415 Magpie-lark Grallina cyanoleuca Magpie-lark
10250 Masked Owl Tyto novaehollandiae novaehollandiae Masked Owl
10564 Mistletoebird Dicaeum hirundinaceum Mistletoebird
11115 Mountain Brushtail Possum Trichosurus cunninghami Mountain Brushtail Possum
11156 Mountain Pygmy-possum Burramys parvus Mountain Pygmy-possum
11412 House Mouse Mus musculus House Mouse
10258 Musk Lorikeet Glossopsitta concinna Musk Lorikeet
10240 Nankeen Kestrel Falco cenchroides Nankeen Kestrel
10631 New Holland Honeyeater Phylidonyris novaehollandiae New Holland Honeyeater
11455 New Holland Mouse Pseudomys novaehollandiae New Holland Mouse
10634 Noisy Miner Manorina melanocephala Noisy Miner
10405 Olive Whistler Pachycephala olivacea Olive Whistler
10249 Pacific Barn Owl Tyto javanica Pacific Barn Owl
10014 Painted Button-quail Turnix varia Painted Button-quail
10337 Pallid Cuckoo Cuculus pallidus Pallid Cuckoo
10237 Peregrine Falcon Falco peregrinus Peregrine Falcon
10700 Pied Butcherbird Cracticus nigrogularis Pied Butcherbird
10694 Pied Currawong Strepera graculina Pied Currawong
11514 Pig (feral) Sus scrofa Pig (feral)
10506 Pilotbird Pycnoptilus floccosus Pilotbird
10383 Pink Robin Petroica rodinogaster Pink Robin
11806 Potoroo Potorous Potoroo
10248 Powerful Owl Ninox strenua Powerful Owl
11803 Pygmy-possums Cercartetus Pygmy-possums
10254 Rainbow Lorikeet Trichoglossus haematodus Rainbow Lorikeet
11818 Rats gen. Rattus Rattus spp.
10837 Ravens and Crows Corvus Ravens and Crows
10638 Red Wattlebird Anthochaera carunculata Red Wattlebird
10662 Red-browed Finch Neochmia temporalis Red-browed Finch
10560 Red-browed Treecreeper Climacteris erythrops Red-browed Treecreeper
10381 Red-capped Robin Petroica goodenovii Red-capped Robin
11261 Red-necked Wallaby Macropus rufogriseus Red-necked Wallaby
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VBA taxon ID Common name Scientific Name Tag
10295 Red-rumped Parrot Psephotus haematonotus Red-rumped Parrot
10264 Red-tailed Black-Cockatoo Calyptorhynchus banksii graptogyne Red-tailed Black-Cockatoo
10603 Regent Honeyeater Anthochaera phrygia Regent Honeyeater
10278 Regent Parrot Polytelis anthopeplus monarchoides Regent Parrot
10369 Restless Flycatcher Myiagra inquieta Restless Flycatcher
NA Reptile unknown Reptile unknown
10384 Rose Robin Petroica rosea Rose Robin
10362 Rufous Fantail Rhipidura rufifrons Rufous Fantail
10509 Rufous Songlark Cincloramphus mathewsi Rufous Songlark
10401 Rufous Whistler Pachycephala rufiventris Rufous Whistler
10326 Sacred Kingfisher Todiramphus sanctus Sacred Kingfisher
11527 Sambar Cervus unicolor Sambar
10679 Satin Bowerbird Ptilonorhynchus violaceus Satin Bowerbird
10366 Satin Flycatcher Myiagra cyanoleuca Satin Flycatcher
10586 Scarlet Honeyeater Myzomela sanguinolenta Scarlet Honeyeater
10380 Scarlet Robin Petroica boodang Scarlet Robin
11522 Sheep (feral) Ovis aries Sheep (feral)
10344 Shining Bronze-Cuckoo Chrysococcyx lucidus Shining Bronze-Cuckoo
10574 Silvereye Zosterops lateralis Silvereye
11458 Smoky Mouse Pseudomys fumeus Smoky Mouse
10992 Song Thrush Turdus philomelos Song Thrush
10253 Sooty Owl Tyto tenebricosa tenebricosa Sooty Owl
10242 Southern Boobook Ninox novaeseelandiae Southern Boobook
61092 Southern Brown Bandicoot Isoodon obesulus obesulus Southern Brown Bandicoot
10504 Speckled Warbler Chthonicola sagittatus Speckled Warbler
11008 Spot-tailed Quoll Dasyurus maculatus maculatus Spot-tailed Quoll
10218 Spotted Harrier Circus assimilis Spotted Harrier
10565 Spotted Pardalote Pardalotus punctatus Spotted Pardalote
10436 Spotted Quail-thrush Cinclosoma punctatum Spotted Quail-thrush
10230 Square-tailed Kite Lophoictinia isura Square-tailed Kite
11008 Spot-tailed Quoll Dasyurus maculatus maculatus Spot-tailed Quoll
10976 Striated Pardalote Pardalotus striatus Striated Pardalote
10470 Striated Thornbill Acanthiza lineata Striated Thornbill
10009 Stubble Quail Coturnix pectoralis Stubble Quail
11138 Sugar Glider Petaurus breviceps Sugar Glider
10269 Sulphur-crested Cockatoo Cacatua galerita Sulphur-crested Cockatoo
10529 Superb Fairy-wren Malurus cyaneus Superb Fairy-wren
10350 Superb Lyrebird Menura novaehollandiae Superb Lyrebird
10277 Superb Parrot Polytelis swainsonii Superb Parrot
11034 Swamp Antechinus Antechinus minimus maritimus Swamp Antechinus
10219 Swamp Harrier Circus approximans Swamp Harrier
11398 Swamp Rat Rattus lutreolus Swamp Rat
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VBA taxon ID Common name Scientific Name Tag
10309 Swift Parrot Lathamus discolor Swift Parrot
10313 Tawny Frogmouth Podargus strigoides Tawny Frogmouth
10027 Topknot Pigeon Lopholaimus antarcticus Topknot Pigeon
10359 Tree Martin Petrochelidon nigricans Tree Martin
10302 Turquoise Parrot Neophema pulchella Turquoise Parrot
11821 Dasyurids Dasyuridae Dasyurids
11813 unidentified Pseudomys gen. Pseudomys Unidentified Pseudomys
10549 Varied Sittella Daphoenositta chrysoptera Varied Sittella
11415 Water Rat Hydromys chrysogaster Water Rat
10224 Wedge-tailed Eagle Aquila audax Wedge-tailed Eagle
10465 Weebill Smicrornis brevirostris Weebill
10357 Welcome Swallow Petrochelidon neoxena Welcome Swallow
10228 Whistling Kite Haliastur sphenurus Whistling Kite
10425 White-bellied Cuckoo-shrike Coracina papuensis White-bellied Cuckoo-shrike
10543 White-breasted Woodswallow Artamus leucorynchus White-breasted Woodswallow
10488 White-browed Scrubwren Sericornis frontalis White-browed Scrubwren
10561 White-browed Treecreeper Climacteris affinis White-browed Treecreeper
10545 White-browed Woodswallow Artamus superciliosus White-browed Woodswallow
10617 White-eared Honeyeater Lichenostomus leucotis White-eared Honeyeater
11069 White-footed Dunnart Sminthopsis leucopus White-footed Dunnart
10448 White-fronted Chat Epthianura albifrons White-fronted Chat
10028 White-headed Pigeon Columba leucomela White-headed Pigeon
10578 White-naped Honeyeater Melithreptus lunatus White-naped Honeyeater
10625 White-plumed Honeyeater Lichenostomus penicillatus White-plumed Honeyeater
10453 White-throated Gerygone Gerygone olivacea White-throated Gerygone
10334 White-throated Needletail Hirundapus caudacutus White-throated Needletail
10330 White-throated Nightjar Eurostopodus mystacalis White-throated Nightjar
10558 White-throated Treecreeper Cormobates leucophaeus White-throated Treecreeper
10693 White-winged Chough Corcorax melanorhamphos White-winged Chough
10364 Willie Wagtail Rhipidura leucophrys Willie Wagtail
10044 Wonga Pigeon Leucosarcia melanoleuca Wonga Pigeon
10471 Yellow Thornbill Acanthiza nana Yellow Thornbill
11136 Yellow-bellied Glider Petaurus australis Yellow-bellied Glider
10614 Yellow-faced Honeyeater Lichenostomus chrysops Yellow-faced Honeyeater
10486 Yellow-rumped Thornbill Acanthiza chrysorrhoa Yellow-rumped Thornbill
10267 Yellow-tailed Black-Cockatoo Calyptorhynchus funereus Yellow-tailed Black-Cockatoo
10619 Yellow-tufted Honeyeater Lichenostomus melanops Yellow-tufted Honeyeater