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ImageJ can be downloaded from the ‘Downloads’ page at https://imagej.net,
though you may also need to download the ‘cell counter’ plug-in for manual counts.
Alternatively, if you download ‘Imagej Fuji’, this comes with a wide range of plugins already incorporated, including the cell counter. ImageJ Fuji can be downloaded
at https://imagej.net/Fiji/Downloads. A user guide is also freely available (Ferreira
and Rasband 2012).
Case Study and Image Locations
The species and locations selected for case studies were those illustrated in Figs. 2,
3, 4 and 5, namely:
• Guillemots (Uria aalge) at their Elegug Stacks breeding colony in Pembrokeshire,
UK;
• Greater Flamingos (Phoenicopteris roseus) on their wintering grounds at Doñana
National Park in Andalucia, Spain;
• Golden Plovers (Pluvialis apricaria) and Linnet (Carduelis cannabina) flocks on
farmland in the Angle Peninsula in Pembrokeshire, UK; and
• Starlings (Sturnus vulgaris) murmurating near a roost on the pier at Aberystwyth
in Ceredigion, UK.
These case studies illustrate the potential of ImageJ for providing accurate estimates of bird numbers from images taken in a variety of different situations.
Methods
ImageJ can carry out either manual or automatic counts as appropriate, depending
on the number and density of the birds in the image and on the complexity of the
background. The sections below detail the key stages in the process, namely:
1. Image collection;
2. Deciding whether to carry out a manual or automatic bird count in ImageJ;
3. The process for carrying out counts in ImageJ;
4. Validating the counts.
Image Collection
Three key components of the image collection process combine to provide suitable
images for carrying out bird counts in ImageJ: these are the camera equipment, the
camera settings and the method of image capture.
C. Hurford
ImageJ can be downloaded from the ‘Downloads’ page at https://imagej.net,
though you may also need to download the ‘cell counter’ plug-in for manual counts.
Alternatively, if you download ‘Imagej Fuji’, this comes with a wide range of plugins already incorporated, including the cell counter. ImageJ Fuji can be downloaded
at https://imagej.net/Fiji/Downloads. A user guide is also freely available (Ferreira
and Rasband 2012).
Case Study and Image Locations
The species and locations selected for case studies were those illustrated in Figs. 2,
3, 4 and 5, namely:
• Guillemots (Uria aalge) at their Elegug Stacks breeding colony in Pembrokeshire,
UK;
• Greater Flamingos (Phoenicopteris roseus) on their wintering grounds at Doñana
National Park in Andalucia, Spain;
• Golden Plovers (Pluvialis apricaria) and Linnet (Carduelis cannabina) flocks on
farmland in the Angle Peninsula in Pembrokeshire, UK; and
• Starlings (Sturnus vulgaris) murmurating near a roost on the pier at Aberystwyth
in Ceredigion, UK.
These case studies illustrate the potential of ImageJ for providing accurate estimates of bird numbers from images taken in a variety of different situations.
Methods
ImageJ can carry out either manual or automatic counts as appropriate, depending
on the number and density of the birds in the image and on the complexity of the
background. The sections below detail the key stages in the process, namely:
1. Image collection;
2. Deciding whether to carry out a manual or automatic bird count in ImageJ;
3. The process for carrying out counts in ImageJ;
4. Validating the counts.
Image Collection
Three key components of the image collection process combine to provide suitable
images for carrying out bird counts in ImageJ: these are the camera equipment, the
camera settings and the method of image capture.
C. Hurford