PerkinElmer RAW files

ImageJ Macro collection for PerkinElmer Ultraview RS RAW-files

Author:

T. Zimmermann, K. Miura + S. Terjung ALMF @ EMBL Heidelberg

Date:

2004/09/20: first version
2004/11/04: improved loading (faster + no more flickering windows), export to tif added
2004/11/07: slicing in depth projections corrected
2004/11/12: 2D time-lapse optimized
2004/12/15: 2 channel bugfix
2005/03/23: Importing RAW file "16-bit Signed" changed to "16-bit Unsigned" to avoid adding artificial offsets.
2006/02/03: Tif export now write filenames which Imaris sorts correctly into channels, timepoints and sections. Additional functions to export tifs with ‘swapped bytes’ (plugin
‘byte swapper’ needed!) which are loadeded correctly by Imaris 4.1.3 + 4.5.2 .
2006/03/23: added extra file types to determine_etcfiles_kota(filename)
2006/03/31: solve the problem of underscore containing file name prefix.
                 the prefix is esolved by counting the last position from "." where as the
                 previous version considered the first underscore as the ending of the prefix.
                 changed:function returnPerkEl_SliceNum(fullfilename)
                 function returnPerkEl_Prefix1(fullfilename)

Source:

PerkinElmer_raw_060331.txt

Installation:

Download PerkinElmer_raw_060331.txt to the ImageJ macro folder (click with your right mouse button on the link and choose “save target link as”).
To install it, open ImageJ and choose:
ImageJ Menu...Plugins...Macro...Install... (and choose the desired macro)

Description:

This is a collection of macros to import and process image series in the generic (raw) file format of the Perkin Elmer Ultraview RS Software. The files are RAW files with a 6 byte offset and little-endian byte order.
The 3D stacks are loaded sequentially which enables the processing of large series even with small RAM.

Don´t use space characters in the path or filenames!

Functions:

Projections
Make Timelapse 1 channel:
This macro loads the raw data files of a 1 channel 2D time-lapse into one stack.

Make Timelapse 2 channel:
This macro loads the raw data files of a 2 channel 2D time-lapse into one stack for each channel

Make projections 1 channel:
This macro loads the raw data files of a 1 channel 3D time-lapse and z-projects it into one stack.

Make projections 2 channel:
This macro loads the raw data files of a 2 channel 3D time-lapse and z-projects it into one stack for each channel.

Make color coded projections 1 channel:
This macro loads the raw data files of a 1 channel 3D time-lapse and z-projects it depth color coded into one RGBstack.

Make color coded projections 2 channel:
This macro loads the raw data files of a 2 channel 3D time-lapse and z-projects it depth color coded into one RGBstack for each channel.

Export to Tiff-files
Batch Convert 3D 1 Channel (among 2 channels) to Tiff:

Batch Convert 3D 2 Channel to Tiff:
Converts a 3D 2 Channel data set (raw-files) to tiff-files. The user can choose a destination folder for each channel.

Batch Convert 3D 2 Channel to 8bit Tiff:
As above but with conversion to 8bit. The user supplies the upper and lower grayvalues of the original series which will correspond to 255 and 0 in the 8bit files, respectively.

Batch Convert 3D 2 Channel to half resized Tiff:
Also converts raw to tiff but the images are downscaled to 50% in x- and y-direction.

Batch Convert 3D 2 Channel to half resized 8bit Tiff:
Conversion from raw to tiff with downscaling to 50% and 8bit.

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