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manual count of the Guillemot colony in ImageJ: this process was the same for the
manual counts carried out for validation purposes in Case Studies 3, 4, 5 and 6. In the
‘automatic count’ mode, ImageJ will generate a relatively accurate count of several
thousands of birds in seconds, a task that could take many hours, if not days, to carry
out manually. However, the accuracy of the count will depend entirely on a) the ability
of the program to isolate the birds from their background, b) the threshold settings
applied to the image and c) the pixel range settings applied to the image.
To deliver a near-accurate automatic count, ImageJ needs an image that shows
clearly defined bird outlines against a clean and high contrast background: each bird
needs to be a separate entity, i.e. something that the program can equate to a blood
cell. Case Study 2 below outlines the process for carrying out an automatic count in
ImageJ and the subsequent case studies illustrate how to adjust the automatic count
settings to different situations.
Text Box 1: The Process and Settings Used for Carrying Out the ImageJ
Manual Count of the Guillemots at the Elegug Stacks Colony in
Pembrokeshire, UK
Open ImageJ, select File ➾ Open – and choose the image that you want to
analyse
When the image is open in ImageJ select Plugins ➾ Analyze ➾ Cell
counter
This will open a table showing the cell counter options, click on ‘Initialize’
Next, choose your ‘Counter Type’ for the species that you want to count –
some of the markers colours are brighter than others, so you might want to test
them before deciding which to use. If there is more than one species in the
image, select a different ‘Counter Type’ for species that you want to count.
After selecting the Counter Type, just left-click on each individual that you
want to count and ImageJ will leave a marker on the bird to show that it has
been counted and will add one to the total for that marker type, so you do not
need to count and cannot lose your place in the image. Note that you can
zoom into the image using the ‘zoom’ option under the ‘Image’ heading in the
main menu and you can move about the image while counting by toggling
between the ‘hand’ scrolling tool and the point selection tool on the main
menu.
When you have finished counting, click on ‘Results’ in the cell counter
table and an Excel spreadsheet will pop up showing how many species of each
type you have counted, click on ‘File’➾‘Save’ to save these results in your
chosen location
Click on ‘Export’ and your image will pop up with the markers on it
In the main ImageJ menu select ‘File’ ➾‘Save as’ – then choose the image
type from the drop-down menu, e.g. Tiff or Jpeg etc
Finally, choose a file name and location and click on ‘Save’
Improving the Accuracy of Bird Counts Using Manual and Automated Counts…
manual count of the Guillemot colony in ImageJ: this process was the same for the
manual counts carried out for validation purposes in Case Studies 3, 4, 5 and 6. In the
‘automatic count’ mode, ImageJ will generate a relatively accurate count of several
thousands of birds in seconds, a task that could take many hours, if not days, to carry
out manually. However, the accuracy of the count will depend entirely on a) the ability
of the program to isolate the birds from their background, b) the threshold settings
applied to the image and c) the pixel range settings applied to the image.
To deliver a near-accurate automatic count, ImageJ needs an image that shows
clearly defined bird outlines against a clean and high contrast background: each bird
needs to be a separate entity, i.e. something that the program can equate to a blood
cell. Case Study 2 below outlines the process for carrying out an automatic count in
ImageJ and the subsequent case studies illustrate how to adjust the automatic count
settings to different situations.
Text Box 1: The Process and Settings Used for Carrying Out the ImageJ
Manual Count of the Guillemots at the Elegug Stacks Colony in
Pembrokeshire, UK
Open ImageJ, select File ➾ Open – and choose the image that you want to
analyse
When the image is open in ImageJ select Plugins ➾ Analyze ➾ Cell
counter
This will open a table showing the cell counter options, click on ‘Initialize’
Next, choose your ‘Counter Type’ for the species that you want to count –
some of the markers colours are brighter than others, so you might want to test
them before deciding which to use. If there is more than one species in the
image, select a different ‘Counter Type’ for species that you want to count.
After selecting the Counter Type, just left-click on each individual that you
want to count and ImageJ will leave a marker on the bird to show that it has
been counted and will add one to the total for that marker type, so you do not
need to count and cannot lose your place in the image. Note that you can
zoom into the image using the ‘zoom’ option under the ‘Image’ heading in the
main menu and you can move about the image while counting by toggling
between the ‘hand’ scrolling tool and the point selection tool on the main
menu.
When you have finished counting, click on ‘Results’ in the cell counter
table and an Excel spreadsheet will pop up showing how many species of each
type you have counted, click on ‘File’➾‘Save’ to save these results in your
chosen location
Click on ‘Export’ and your image will pop up with the markers on it
In the main ImageJ menu select ‘File’ ➾‘Save as’ – then choose the image
type from the drop-down menu, e.g. Tiff or Jpeg etc
Finally, choose a file name and location and click on ‘Save’
Improving the Accuracy of Bird Counts Using Manual and Automated Counts…