survey guideline - digikam images (v3) · (e.g. you can only see a furry blur or a tail). these...

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

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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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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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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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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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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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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

survey guideline - digikam images (v3) · (e.g. you can only see a furry blur or a tail). these...

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