All ObjectJ Examples
Marking Growth Rings in Fish Otoliths
A project for interactive analysis of otoliths with ImageJ and ObjectJ
Instruction Video (3:50 min)
The instruction video covers the following sequence
- Make sure plugin "ObjectJ" is loaded under ImageJ>Plugins
(You can install ObjectJ by dragging objectj_.jar onto the ImageJ main window and then confirm to store it in ImageJ's plugins directory)
For trying out, a folder with two demo otolith images is available
- Put a copy of Otoliths_xx.ojj into the folder that contains the images to be annotated
- Open Otoliths_xx.ojj by dragging it into the ImageJ main window
- ObjectJ menu becomes visible
- Link the images to be measured by dragging them into the panel for Linked Images
- Open the first image by double-clicking its name in the panel for linked images
- ObjectJ menu contains four embedded macro commands at the bottom:
- Choose ObjectJ>Start Sequence [F1]
- In ObjectJ Tools, "Core" is selected and cursor becomes green
- Mark the green Core line
- In ObjectJ Tools, "Vector" is automatically selected and cursor becomes red
- Mark the red Vector line
- In ObjectJ Tools, "Increment" is automatically selected and cursor becomes blue
- Mark the increments (in any order). Press key Backspace to delete the last point
- Finish the sequence by choosing ObjectJ>Year and Quality...[F2]
- Enter the start year as positive number, or the end year as negative number
- The sequence is now complete. Optionally, choose ObjectJ>Show/Hide Year Annotation
- The annotation is a temporary ImageJ overlay which needs not to be saved
- Continue to measure more otoliths
- Choose ObjectJ>Save project which updates the .ojj project file.
- Choose ObjectJ>Show ObjectJ Results to observe the results
- Choose ObjectJ>Create Output Table for specially formatted output
- The colored overlay (Core, Vector, Increments) is not saved as part of the image, it is stored in the .ojj project file. The year numbers are not saved as overlay - they are re-built when needed.
- You can "link" more images and continue marking at a later time.
- Also at a later time, you can perfrom corrections: change the position of any marked point by selecting the "triangle" tool in ObjecJ Tools, and keep the "alt' key down while moving the point.
Similarly, you can delete an entire object with the pistol tool, or keep key "alt" key down to delete a point only.
When choosing ObjectJ>Create Output Table, the blue "Increment" points will be arranged in the correct order and snap onto the red Vector line before the table is created.
- You also can change the scaling of linked .tif or .jpg images: choose ObjectJ>Show Project Window> Images and right-click and change any field in column "px/unit". Results will be updated.
- The contents of the table can optionally be adjusted via the embedded macros.
The current sturcture is shown below:
by Côme Denechaud