Batch Processing Macro

4D Time Series Batch Processing macro collection for ImageJ

 

Author:

K. Miura, EMBL Heidelberg, Germany

Date:

2004/09/01
2005/01/14:
   source files can now be 8 or 16 bit
   window pop-up suppression in batch mode
   file list analyzer
   additional filename convention implemented

Source:

4D_PE_processor.txt

Installation:

Download 4D_PE_processor.txt (e.g. click with right mouse button and select ‘save target link as’) to the macro folder and install it:
ImageJ Menu...Plugins...Macro...Install... Choose 4D_PE_processor.txt in the ImageJ macro folder

Description:

This macro loads single 3D stacks of a 4D time series sequentially to perform one of the following operations on it:

1) Zprojection (average, maximum or minimum projection along Z-axis)
2) resizing (changing the pixel number)
3) enhance contrast 
4) gamma correction

This batch processing enables to work with very large series.

Additional Description

Prerequisite:
ImageJ version 1.33s or higher. The filename follows the convention prefix1_Txxxx_prefix2_Zxxxx.tif (e.g. myExp_T0002_488nm_Z1234.tif) or prefix1_xxxx_xxx.tif (e.g. AGHEMO_0002_001.tif). This format is used for example by the export function of the PerkinElmer Ultraview software.

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