All ObjectJ Examples

ObjectJ Cell Counter

Norbert Vischer
University of Amsterdam
09-oct-2013

ObjectJ Cell Counter is a simple example for manual cell counting.

Features:
- 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 Small,Big,Double
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.


A. Installation of ImageJ and ObjectJ:

  1. If not yet done, install ImageJ from: http://imagej.nih.gov/ij/

  2. 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:
    simon.bio.uva.nl/objectj/download/current/objectj_.jar

  3. ImageJ then fetches objectj_.jar and suggests to store it in the plugins folder.
    Confirm by clicking the Save button, Quit and Relaunch ImageJ.

  4. 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.


B. Run the Demo Project:

  1. Download and unpack the demo project from:
    http://simon.bio.uva.nl/objectj/examples/CellCounter/CellCounterProject.zip
    It includes a project file (ending with .ojj) and two 'Blob' images for demonstration.

  2. Open file Cell-Counter.ojj by dragging it into the ImageJ main window (or use File> Open..)

  3. 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.

  4. This project contains embedded macros that appear under the ObjectJ menu:
    Keyboard shortcuts [1], [2] and [3] have the same effect as selecting an item in ObjectJ Tools:
    ObjectJ> Small [1]
    ObjectJ> Big [2]
    ObjectJ> Double [3]
    ObjectJ> Update Initials [7] Draws initials next to markers in front image (here: S, B or D).
    ObjectJ> Update Labels [8] Draws entire item names next to markers in front image.
    ObjectJ> Remove Labels [9] 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

  5. Now select an item in ObjectJ Tools and place additional markers into image blob_2.tif.

  6. Important: The Composite checkbox in ObjectJ Tools must not be turned on, otherwise subsequent marking will accummulate several items in one object.
  7. In this demo, numerical labels in Project Window> Objects are switched off so the don't interfere with text labels.
  8. You can add more image files to the project folder and drag them from there into the Project Window> Images Panel.
  9. Choose ObjectJ> Save Project to save the .ojj project file. You don't need to save any images.


C. Modify this project for your needs:

  1. 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.

  2. Open MyProject.ojj (this will close the previous project).

  3. 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.

  4. The demo project includes some simple embedded macros.
    You can change this text by choosing ObjectJ> Show Embedded Macros
    and change the terms Small , Big, 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

  5. Link Images to be marked via ObjectJ> Linked Images.., or by dragging them into the panel for linked images.

  6. Now you are ready to start manual marking.