Concept

Markers are stored in a project file

ObjectJ allows images to be superimposed with graphical objects that appear as colored markers. Markers are non-destructive and are typically distributed over many images or stacks. They are stored in a separate project file such as "MyProject.ojj". This file also holds pointers to linked images - they must reside in the same folder as the project file. Further, the project file contains a results table that is independent of the ImageJ results.

What means "Save" ?

It is important to realize that the screen typically shows two different types of information: i) the image, and ii) the superimposed colored markers. These two parts are stored in different files. For example, after some image processing, you would save a changed image via File>Save. On the other hand, if you have placed markers manually or automatically into an image, you would save the changed set of markers by choosing ObjectJ>Save Project, while the image remains unchanged.

What are objects?

In ObjectJ, an object is a collection of vectorized markers, that are linked to a certain image. An object can be composite, i.e. consist of different items, just like a molecule can contain various elements. Objects carry number labels, starting at 1. The numbers are contiguous within an image. (The term "cell", as used in the former application "Object-Image", is not used anymore).

What are items?

An item is part of an object and consists of a collection of points; it belongs to a certain item type. If you compare an object with a molecule, an item would correspond to an atom. The item type defines appearance such as shape (e.g. point, line, segmented line, polygon, roi), color and marker type.

Results table

The ObjectJ results table is independent of the ImageJ results table; it is stored as part of the project file. Each row of the linked results table is connected to the object with the same number. The user can append any number of columns; either automatic columns that dynamically hold e.g. the length of a line, or columns that hold results calculated by macro using any algorithm.
Besides the linked results, there is also an unlinked results table, whose entries are not connected to any marked objects.

ObjectJ Tools

This window is important for manual marking. Here you can pick your user-defined shapes that are suitable to mark butterfly wings, tree rings or fish larvae. Or use tools to edit or delete existing markers.

Project Macros

Macros are embedded into the project file.
Embedded macro commands appear under the ObjectJ menu, where they can be accessed without navigating through submenus, and where they are not affected by standard ImageJ macros. You can display, edit and re-install these macros via "ObjectJ>Show Embedded Macros".

Structure of a project file

Project files (".ojj" files) are saved binary (optionally as .XML). The project file contains marker positions, item definitions, columns, qualifiers- practically everything except the images themselves. Technically, the .ojj file is a zipped folder containing two files, data and macro. To prevent that other programs (Explorer!) unpack this program, 4 spoiler characters 'o','j', 'j', 0x0) are added to the beginning of the file.


 Tips

Download

Download the newest version of objectj_.jar

Installation

Drag objectj_.jar onto ImageJ's main window (which contains the tools). ImageJ will then suggest to save the jar file in the plugins folder- confirm (or choose a sub-folder).
(If ObjectJ was already active, e.g. when overwriting an older objectj_.jar file, then you need to relaunch ImageJ).
When choosing menu Plugins>ObjectJ, the ObjectJ menu will appear (between "Analyze" and "Plugins").
ObjectJ will automatically be installed if a project file (.ojj extension) is opened.

Do not move the project file

Avoid changing the file path of the ".ojj" project in Finder/Explorer while that project is open.

Double-clicking .ojj files in Finder/Explorer

You can double-click a project file (which has the .ojj extension). Both OS X Finder and Windows Explorer will correctly launch ImageJ, load the ObjectJ plugin, and then open the project file. However, following conditions must be true:
- objectj_.jar must be in the plugins folder
- at least these versions must be used: ObjectJ 0.96x and ImageJ 1.43f
- the .ojj extension must already be associated to the ImageJ application.

Associating .ojj files to ImageJ in OS X Finder:
- select an .ojj file in the Finder
- choose menu File>Get Info
- Select "Open with:"
- as ImageJ doesn't appear in the drop-down menu, choose "Other.."
- navigate to the application ImageJ.app or ImageJ64.app
- click the "Change All.." button
- in the Dialog "Are you sure.." click "Continue
- I recommend to keep the extension visible (uncheck "Hide extension")
Associating .ojj files to ImageJ in Windows 7 Explorer:
- double-click a project file (with extension ".ojj")
- If message appears: "Windows can't open this file", then:
- choose "Select a program from a list of programs"
- If "ImageJ Launcher" does not appear as option, navigate to ImageJ.exe and click "Open"
- Now, "ImageJ Launcher" should appear: Select it.
- check "Always use the selected program.." and click OK
- Now .ojj files are double-clickable and have a black microscope icon.


- Once a file type is associated, the extension (here: .ojj) may be hidden
- You can turn it on by opening an Explorer window, ,
- Choose "Organize > Folder and Search Options
- Select the View tab
- Turn off "Hide Extensions for known file types"
- Click "Apply to Folders"
- Click OK, and again click OK
- .

Function Keys in OS X Finder

OS X by default occupies function keys (F1, F2..) for e.g. screen brightness or speaker volume. To use these keys in a program, you additionally would have to keep down the "fn" key.
For faster operation, select "Use F1, F2.. as standard function keys" in System Preferences>Keyboard & Mouse> . Now the "fn" key is needed for brightness etc, but not for shortcuts in ImageJ/ObjectJ.

Scaling of jpg images

Scientific scaling information (pixels per unit) of a JPG image is normally lost when you close it's window. However, if the image is linked to the current project file, ObjectJ will remember scaling and automatically apply it next time you open it. This also applies for other formats like gif etc.
How to scale a linked image:
- Open a linked image by double-clicking it's name in the "Images" panel
- Apply a scale (pixels/unit) either via Analyze>Set Scale, or via Image>Properties
- In the ObjectJ project window, the column "px/unit" will be updated
- ObjectJ>Save Project will save the scaling and apply it next time the JPG image is opened from within the project.
- Warning: avoid the "global" checkbox in "Set Scale", because it silently re-scales anything that is open now or later - this will not work with ObjectJ.
- Bug: opening an image other than via the ObjectJ panel or ObjectJ menu or an ObjectJ macro will not apply the scaling. This needs to be fixed.