All ObjectJ Examples
Bacterial Cell Biology
University of Amsterdam
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StampFishEggs is a project for manaul classification of fish eggs.
It runs under ImageJ in combination with plugin ObjectJ.
Task: In this marine research project, fish eggs had to be classified and marked with one of ~100 acronyms. For two types (MAC = Mackerel and HER = herring), additionally the development stage (0..6), the egg diameter, and the diameters of any internal oil droplets had to be acquired.
Solution: The program focusses on optimal support for manual marking. The used macro contains a table of keyboard shortcuts and the corresponding acronyms.
If not done yet, install ImageJ from: http://imagej.nih.gov/ij/
If the ObjectJ plugin is already visible under menu Plugins, jump to (4).
Otherwise, you can install ObjectJ as follows:
Download objectj_.jar from https://sils.fnwi.uva.nl/bcb/objectj/download/current/
objectj_.jar was not renamed (because an older version already existed in the download folder).
objectj_.jar onto ImageJ's main window (which contains the tools).
Confirm when ImageJ asks to store this plugin in the plugins folder, and relaunch ImageJ.
You can choose Plugins> ObjectJ to make the ObjectJ menu visible (see fig 2),
but the ObjectJ menu will appear anyway the first time you open an
.ojj project file.
In order to open StampFishEggs_xx.ojj, you can either drag its file icon from the Finder/Explorer into the main window with title "ImageJ", or you can use ImageJ's Open menu.
If the ObjectJ menu (between Analyze and Plugins, Fig 2) was not visible yet, it should appear now.
Now the project window is shown. If the panel for linked images is still empty, link images by dragging them in Finder or Explorer into the panel for linked images. Alternatively, you can link images via menu ObjectJ>Linked Images.
Green bullets confirm that the image files are in the same folder as the project.
Double-click the first image to open it.
Subsequently, "mac-2" eggs can be marked by positioning the cursor at the top of a Mackerel-2 egg, and matching the circular roi with the outer egg contour, as mac-2 is of type "Shell". If the mouse is clicked inside an existing egg, this is interpreted as one of the cell's oil droplet. (If two cells overlap, keep alt key down to avoid oil marking).
Opens the Code Table, that reflects the shortcut definitions and their species labels. Additionally, it opens and updates the ObjectJ "Linked Results" tables. In contrast, choosing ObjectJ>Show ObjectJ Results does not update columns Spec and Stage
Activates the Egg Tool (E) in ObjectJ Tools. This is a preparation for marking eggs. At the same time, a 1.5 sec flash appears close to the cursor to indicate currently preselected egg type.
This is a shortcut for selecting the pistol tool in ObjectJ Tools, which is used to kill entire objects, or (with the shift key down) items such as an oil droplet.
This is a shortcut for selecting the Finger tool in ObjectJ Tools. With the finger tool, you can select an object.
To use label names that are not listed in the shortcut label, choose "ObjectJ>Exotic [X]" to enter a special name. Previous exotics may appear as radio buttons to bereused without typing. You also can enter names that are already defined in the code table.
Menu "Rename Objects" can be used to change the name of existing objects. The new name needs not to be in the code table. If you check "Confirm", each egg will be shown in zoomed mode before you click Yes or No.
"Key" menu should be ignored by the user, but it is necessary to accommodate 20 keystroke shortcuts (keys 0-9, and keys n0-n9 from the numerical keypad). You cannot choose such a key from the menu because the mouse location is used to locate the fish egg.
Left: Code table:
|Species:||Label used for overlay|
|Shape:||"Shell" for circular contour, "Spot" for single point marker|
|Column Freq:||Shows count of corresponding category|
Right: This macro code was used to define the code table shown on the left. When altering this for your needs, choose single digits for the most frequent species. Example: "her" is marked after pressing single digit "4". If another shortcut would try to use "41", the program would report an error.
|Cat||Category, name of the acronym used as labes|
|Spec||Name of species, same as "cat" before the dash|
|Stage||Development stage, digit after the dash in Cat|
|EggDia||Diameter of egg if it was measured|
|nOil||number of oil droplets|
|OilDia1||Diameter of oil droplet #1|
|OilDia2||Diameter of oil droplet #2|
|OilDia3||Diameter of oil droplet #3|
|OilDia4||Diameter of oil droplet #4|