All ObjectJ Examples
University of Amsterdam
ObjectJ Cell Counter is a simple example for manual cell counting.
- Cursor color reflects current cell type
- Pistol tool for deleting markers
- Mark many images or (hyper)stacks using a single project file
- No duplicates of images and no additional files are created
- Mark TIF or non-TIF files
- Adjustable names, marker types and text labels
In this example, we use three marker names
for marking Blobs. The output is displayed in a simple table.
Configuring the linked ObjectJ Results table for more complex output is not described here.
If not yet done, install ImageJ from: http://imagej.nih.gov/ij/
If the ObjectJ plugin is already installed (i.e. visible under menu Plugins), jump to (4).
Otherwise, you can install ObjectJ as follows:
In ImageJ, choose menu File> Import> URL... and type:
ImageJ then fetches
objectj_.jar and suggests to store it in the plugins folder.
Confirm by clicking the Save button, Quit and Relaunch ImageJ.
You can choose Plugins> ObjectJ to make the ObjectJ menu visible (see below),
but opening a project file with extension:
.ojj will also insert this menu.
Download and unpack the demo project from:
It includes a project file (ending with
.ojj) and two 'Blob' images for demonstration.
Open file Cell-Counter.ojj by dragging it into the ImageJ main window (or use File> Open..)
If the ObjectJ menu was not visible yet, it should appear now.
The ObjectJ project window (see fig) indicates two linked images (blob_1.tif and blob_2.tif).
Double click e.g. on blob_2.tif to open this image for further marking.
This project contains embedded macros that appear under the ObjectJ menu:
Keyboard shortcuts ,  and  have the same effect as selecting an item in ObjectJ Tools:
ObjectJ> Small 
ObjectJ> Big 
ObjectJ> Double 
ObjectJ> Update Initials  Draws initials next to markers in front image (here: S, B or D).
ObjectJ> Update Labels  Draws entire item names next to markers in front image.
ObjectJ> Remove Labels  Removes text labels next to markers in front image.
By default, keep these item names disabled as they are not automatically updated.
ObjectJ> Show Count Results Displays counts per image and type
Now select an item in ObjectJ Tools and place additional markers into image
.ojjproject file. You don't need to save any images.
Make a duplicate of the demo project file via ObjectJ> Project> Save an Empty Copy..
(let's call it:
MyProject.ojj) and store it in the same folder as your images to be marked.
MyProject.ojj (this will close the previous project).
Choose ObjectJ> Show Project Window and select the Objects panel.
Here you can modify names and appearnace your item types.
Use Show Object Label to show/hide numerical labels.
The demo project includes some simple embedded macros.
You can change this text by choosing ObjectJ> Show Embedded Macros
and change the terms
Double so they match your new item types,
or adjust appearance of text labels.
Click button Install in ObjectJ Menu, and save the project via ObjectJ> Save Project
Link Images to be marked via ObjectJ> Linked Images.., or by dragging them into the panel for linked images.