UCSD Confocal Microscopy Plugins

Authors: Patrick Kelly and Harvey J. Karten
History: 2000/11/15:
2001/02/22: Updated to work with ImageJ 1.21
2001/10/23: Bug fixes
2001/02/22: Updated to work with ImageJ 1.26
2003/02/21: Bug fixes
2003/11/20: Fixed "Z Projection" option in FVControl
2010/08/12: Updated to work with ImageJ 1.43
Requires: ImageJ 1.43 or later
Source: Included in the ucsd-plugins.zip archive
Installation: Expand the ucsd-plugins.zip archive in the plugins folder and restart ImageJ. The plugins will be listed in the "UCSD Plugins" submenu of the Plugins menu.
Description: This is a set of 10 plugins from the University of California at San Diego that are designed to support microscopy work. The individual plugins are described below.

A sample image from a 12 bit confocal microscope is available. It is a single plate with three channels. Each channel is a separate 16 bit image, with a separate 8 bit LUT for display on the screen.

  1. Open the "FV Control" plugin.
  2. Select "Open Fluoview Image" on the FV controller.
  3. Select the sample image (fluoview.tif ).
  4. Play with the FV control to turn various Active channels on and off.
  5. Play with the ROV adjuster which is called from the FV control.
  6. Use the "ExtendedInfo" plugin to read the original information on collection parameters, as well as to show the various details of the 8 bit LUT used for the display of each channel.
  7. Use the Split FV on the FV Control. Notice that each individual slice retains the original 8 bit LUT
  8. Call the "SynchWindows" plugin. Select the original image and all the derived slices. Click on Synchronize all.
  9. When you move a cursor on one image, it will move to the corresponding location on all of the of selected images.
  10. You can directly convert the original file to RGB 24 bit. However, in the original format you could change the gray scale image with the ROV control without altering the image of of any other channel. After converting to RGB you will find that there is no way that you can independently modify the gray scales, as it is now represented in the R,G and B channels.

General Purpose Plugins

Split Stack

Splits an image stack into a user specified number of substacks. Each substack can consist of a single image.



Synchronize mouse motion and input between multiple windows. Thus, an ROI drawn in one window is replicated in all other synchronized windows in the synchronized window set. A synchronization cursor (the red box above) indicates the location of the mouse in all synchronized windows.

Tiff Related Plugins

Extended Info


Similar to ImageJ's standard Image Info plugin filter, but adds displays additional information regarding lookup tables. This plugin is most useful for the Extended Tiff plugin (see below) but will work for standard ImageJ image objects as well. In this case, this plugin simply displays a lookup table if available.

Extended Tiff

Extends ImagePlus class to read additional information from TIFF image files. Currently, this reads TIFF ImageDescription field. ExtendedTiff class also provides a post processing method intended to allow its subclasses to add additional processing to handle nonstandard TIFF images or standard TIFF images in an application specific fashion.

Extended Tiff Encoder

A modified version of standard ImageJ TiffEncoder that also reads the TIFF image description field.

Save Extended Tiff

A plugin that writes an ExtendedTiff file to disk.

Olympus Fluoview Specific Plugins

Clamped Color Model

This class provides an indexed color model that also supports upper and lower bounds on the indices. This allows the indices to be "clamped" to these bounds prior to their use to retrieve color lookup table data. This class is used in the FluoviewTiff plugin, described below, and will probably not be of interest to general uses. However, it must be present to run the FluoviewTiff and related plugins.

Fluoview Tiff


Extends ExtendedTiff class to manage additional information associated with Fluoview Tiff images. This information consists of color table data, intensity mapping parameters and a collection of acquisition parameters. Thus, we can display images, such as that shown above, wherein three (grayscale) channels are colored using the associated color table information and combined into one 24-bit color display.

FV Color Display

Toggles color display mode on/off.

FV Control

This plugin collects a variety of operations that are specific to manipulation of Fluoview images. For instance, users can toggle specific channels on and off. This plugin also provides an integrated interface to Fluoview specific versions of some of the above standard plugins, e.g. Z-projection and stack splitting.

FV Split Stack

A version of the Split Stack plugin that is specifically designed to handle Fluoview images. The Fluoview split stack plugin splits a Fluoview stack into multiple substacks, one for each channel in the original data set. In addition, the Fluoview split stack plugin ensures that appropriate Fluoview channel information is propagated to each of the new stacks.

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