Tony's Plugins

Nuclear Medicine Plugin Collection (tp_collection.jar)

Author: J. Anthony Parker, MD PhD (J.A.Parker@IEEE.org )

Dates: 2008/5/19: First version
2008/5/19: Updated - Fiji collection
2010/4/20: Updated
2010/12/12: Updated
2011/12/23: Updated

Limitations:
Requires Sun's 445k jimi library for some input/output plugins.
Requires the iText library for "PDF Writer" plugin.
Requires QuickTime and QuickTime for Java for QuickTime plugins on non macintosh platforms.

Source: The configuration file used in tp_collection.jar file is plugins.config.txt and in tp_collectionFiji.jar file is pluginsFiji.config.txt.

Installation:
Download:
tp_collection.jar for ImageJ or tp_collectionFiji.jar for Fiji,

jimi.jar (from the ImageJ site), and

the iText library

to the plugins folder and restart ImageJ.

Description:
This collection is intended for Nuclear Medicine users who want to get a quick start on selecting plugins. A more experienced user will likely want to select his/her own set of plugins. Note the most recent date above. If it is a long time ago, there are apt to be more up-to-date versions at the primary locations listed below. If you find this collection useful and would like it updated, please let me know.
The following lists the contents of tp_collection.jar or tp_collectionFiji.jar. A few of these plugins are already included in Fiji.
Input/Output

DICOM Rewriter

DICOM Sort

Excel Writer

Open and Save Images Using Jimi

Jimi Reader

Jimi Writer

QuickTime

QuickTime Movie Writer

QuickTime Opener

PDF Writer

Parker Plugins

Align Stacks

Alignment

Fusion

Orthogonal View Display

Reorient Stack

Show Alignment

To AxialTP

To CoronalTP

To SagitalTP

TwoD HistogramTP

NucMed

3D Project ... Modification

Activity to Moles

Compartmental Analysis

Copy Pixel Size

DICOM Rescale

Dispose All Windows

Fit Line

FoutBy64

Histogram Equalization

Interfile Decoder

Interfile Encoder

Lookup Tables

Origin Preserving Crop

Pixel Size

Radiation-Induced Cancer Risk and Rate (Caner_RateTP)

Reorder Gated Slices

Stack Interleaver

Stacks

Concatenator

Slice Remover (ImageJ only)

Stack Builder

Stack Combiner (ImageJ only)

Stack Inserter (ImageJ only)

Stack Maker (ImageJ only)

Stack Normalizer

Stack Reverser (ImageJ only)

Stack Splitter

Substack Maker (ImageJ only)

See Also:
OME at LOCI - Software - Bio-Formats - ImageJ
Download .jar file (http://www.loci.wisc.edu/software/loci_tools.jar) to plugins and restart. Extensive set of tools supporting input/out formats for microscopy including DICOM and compressed DICOM. From the Open Microspcopy Enviornment (OME) at the Laboratory for Optical and Computational Instrumentation (LOCI). I have not included it in installation due to the size, 7 MB.

FAQ

Tudor DICOM Tools

This toolkit includes both a stand alone DICOM viewer and a set of ImageJ plugins which provide DICOM capabilities. The plugins come as a runable ImageJ package. Although the DICOM package is quite useful, I have not included it in the collection above because the integration is a bit complicated.

MedNuc Plugin collections

Author:	J. Anthony Parker, MD PhD (J.A.Parker@IEEE.org )
Dates:	2008/5/19: First version 2008/5/19: Updated - Fiji collection 2010/4/20: Updated 2010/12/12: Updated 2011/12/23: Updated
Limitations:	Requires Sun's 445k jimi library for some input/output plugins. Requires the iText library for "PDF Writer" plugin. Requires QuickTime and QuickTime for Java for QuickTime plugins on non macintosh platforms.
Source:	The configuration file used in tp_collection.jar file is plugins.config.txt and in tp_collectionFiji.jar file is pluginsFiji.config.txt.
Installation:	Download: tp_collection.jar for ImageJ or tp_collectionFiji.jar for Fiji, jimi.jar (from the ImageJ site), and the iText library to the plugins folder and restart ImageJ.
Description:	This collection is intended for Nuclear Medicine users who want to get a quick start on selecting plugins. A more experienced user will likely want to select his/her own set of plugins. Note the most recent date above. If it is a long time ago, there are apt to be more up-to-date versions at the primary locations listed below. If you find this collection useful and would like it updated, please let me know. The following lists the contents of tp_collection.jar or tp_collectionFiji.jar. A few of these plugins are already included in Fiji. Input/Output DICOM Rewriter DICOM Sort Excel Writer Open and Save Images Using Jimi Jimi Reader Jimi Writer QuickTime QuickTime Movie Writer QuickTime Opener PDF Writer Parker Plugins Align Stacks Alignment Fusion Orthogonal View Display Reorient Stack Show Alignment To AxialTP To CoronalTP To SagitalTP TwoD HistogramTP NucMed 3D Project ... Modification Activity to Moles Compartmental Analysis Copy Pixel Size DICOM Rescale Dispose All Windows Fit Line FoutBy64 Histogram Equalization Interfile Decoder Interfile Encoder Lookup Tables Origin Preserving Crop Pixel Size Radiation-Induced Cancer Risk and Rate (Caner_RateTP) Reorder Gated Slices Stack Interleaver Stacks Concatenator Slice Remover (ImageJ only) Stack Builder Stack Combiner (ImageJ only) Stack Inserter (ImageJ only) Stack Maker (ImageJ only) Stack Normalizer Stack Reverser (ImageJ only) Stack Splitter Substack Maker (ImageJ only)
See Also:	OME at LOCI - Software - Bio-Formats - ImageJ Download .jar file (http://www.loci.wisc.edu/software/loci_tools.jar) to plugins and restart. Extensive set of tools supporting input/out formats for microscopy including DICOM and compressed DICOM. From the Open Microspcopy Enviornment (OME) at the Laboratory for Optical and Computational Instrumentation (LOCI). I have not included it in installation due to the size, 7 MB. FAQ Tudor DICOM Tools This toolkit includes both a stand alone DICOM viewer and a set of ImageJ plugins which provide DICOM capabilities. The plugins come as a runable ImageJ package. Although the DICOM package is quite useful, I have not included it in the collection above because the integration is a bit complicated. MedNuc Plugin collections