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This is a collection of Plugins to import PerkinElmer UltraView(E)RS data into ImageJ.

Source

Perkin_ElmerPan.jar compatible with Image5D 1.1.5

Perkin_ElmerPan.jar compatible with Image5D 1.2.0

Perkin_ElmerPan1.2.2.jar (updated 5.10.2011)

Installation

Make sure that your ImageJ is version 1.37g or later and that you use Java 1.5.0_06 or later.

Download the Perkin_ElmerPan.jar files into your plugin folder of ImageJ (e.g. on my computer c:\ImageJ\plugins).

In addition you need also to download Image5D.jar to your plugin folder. This is really important; otherwise the plug in is not working properly. If you want to browse/edit the source code you will have to unzip the jar file.

Description PE pannel

either Plugins > PerkinElmer or
File > Import

This opens a panel with four buttons. The functionality of each is described below.

open

This opens the raw files acquired with a PerkinElmer Ultraview (E)RS. The parameters (e.g. number of channels, number of slices, number of time points) of the image series are read from the cfg/tim file. The raw-files are imported into a stack and afterwards automatically converted to an Image5D stack.

Attention: If you created a time series of a large volume ImageJ might run out of memory!

Z-project

This opens the raw files acquired with a PerkinElmer Ultraview (E)RS. The parameters (e.g. number of channels, number of slices, number of time points) of the image series are read from the cfg/tim file. The raw-files are imported into a stack and a Maximum Projection along the z-axis is performed for every time point and every channel. The resulting image-stack is converted to an Image5D stack.

Batch Z-projection

You have to select a folder. The plug ins works with all subfolders of this folder if they contain raw data from an PerkinElmer Ultraview (E)RS. The images of every folder are opened, a maximum intensity projection along the z-axis is performed and the resulting stack (one image per channel and time point) is saved as TIFF-stack (if you checked the tick box for saving in addition you also have the option to convert the resulting stack to 8-Bit).

File info

Opens a window where you can find the meta information to the loaded image.

Further information

Just let me know if you have any ideas/needs for further plug ins dealing with data import/handling of PerkinElmer Ultraview (E)RS files. If you have problems in installing/using the plug ins just let us know. Please also don't hesitate to report bugs.