BioformatsConverter - Revision history

JeromeAvondo at 15:30, 25 August 2011

2011-08-25T15:30:49Z

New page

__NOTOC__
[[Image:BioformatsConverterZip.png|256px|thumb]]

=Description=
This software is useful for batch converting microscopy image formats, like STK, LSM, LIE, ZVI etc etc, to OME-TIFF or PNG files. See [http://www.loci.wisc.edu/ome/formats.html this page] for the supported image formats.
The advantage of converting to OME-TIFF over regular TIFF files is that most of the original image metadata is kept in the file.

This tool is written in Java and is based on the [http://www.loci.wisc.edu/software/bio-formats Bioformats Library] developed by the University of Wisconsin-Madison.

It is cross platform so works under Windows, Linux and Mac.

=Installation=

Extract the contents of the zip file to somewhere sensible on your local machine. Then you can place your image files in the '''IN/''' folder. Note you can place files of different image file formats. ie: a mix of LSM, STK etc...

You then double click on the '''runme.bat''' and wait for the program to finish. Or if you are working under Linux/Mac use the '''Runme.sh''' script.

This will save your converted images in the '''OUT/''' directory.

==Configuration==

The program is configured by editing the file called '''Settings.txt'''. This file can be edited by double clicking on it.

You have the following options.

savemode: TIFF

With this option you can either tell it to save as '''TIFF''' or '''PNG''' files.

The second option is only relevant if you are saving as TIFF files. If you are saving as PNG this option has no effect. Also note that if you are saving as PNG files all metadata will be lost.

stackmode: Z_STACK_TIFFS

This option can take the following options: '''SINGLE_TIFFS''', '''Z_STACK_TIFFS''', '''ZC_STACK_TIFFS''' or '''ZCT_STACK_TIFFS'''

SINGLE_TIFFS: this splits the z-series, channels and timepoints as individual tiff files

Z_STACK_TIFFS: this splits the channels and timepoints as individual z-series tiff stack files

ZC_STACK_TIFFS: this splits the timepoints as individual z-series and multichannels tiff stack files

ZCT_STACK_TIFFS: this creates a single tiff stack for the z-series, mutlichannels and timepoints

=Download=

All Platforms: [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/bioformatsConverter_rev3672.zip BioformatsConverter]

=Source Code=

[[Image:Main.java]]

=Author=

* [[Jerome Avondo]]
* [http://www.loci.wisc.edu/software/bio-formats Bioformats Library]

JeromeAvondo at 09:20, 22 September 2010

2010-09-22T09:20:19Z

← Older revision		Revision as of 09:20, 22 September 2010
Line 6:		Line 6:
	The advantage of converting to OME-TIFF over regular TIFF files is that most of the original image metadata is kept in the file.		The advantage of converting to OME-TIFF over regular TIFF files is that most of the original image metadata is kept in the file.

	This tool written in Java and is based on the [http://www.loci.wisc.edu/software/bio-formats Bioformats Library] developed by the University of Wisconsin-Madison.		This tool is written in Java and is based on the [http://www.loci.wisc.edu/software/bio-formats Bioformats Library] developed by the University of Wisconsin-Madison.

	It is cross platform so works under Windows, Linux and Mac.		It is cross platform so works under Windows, Linux and Mac.

JeromeAvondo at 14:25, 22 July 2010

2010-07-22T14:25:19Z

← Older revision		Revision as of 14:25, 22 July 2010
Line 53:		Line 53:

	* [[Jerome Avondo]]		* [[Jerome Avondo]]
			* [http://www.loci.wisc.edu/software/bio-formats Bioformats Library]

JeromeAvondo at 13:27, 14 July 2010

2010-07-14T13:27:07Z

← Older revision		Revision as of 13:27, 14 July 2010
Line 48:		Line 48:
	=Source Code=		=Source Code=

	[[~~File~~:Main.java]]		[[Image:Main.java]]

	=Author=		=Author=

	* [[Jerome Avondo]]		* [[Jerome Avondo]]

JeromeAvondo at 13:25, 14 July 2010

2010-07-14T13:25:49Z

← Older revision		Revision as of 13:25, 14 July 2010
Line 48:		Line 48:
	=Source Code=		=Source Code=

	[[~~Image:~~:Main.java]]		[[File:Main.java]]

	=Author=		=Author=

	* [[Jerome Avondo]]		* [[Jerome Avondo]]

JeromeAvondo at 13:25, 14 July 2010

2010-07-14T13:25:03Z

← Older revision		Revision as of 13:25, 14 July 2010
Line 48:		Line 48:
	=Source Code=		=Source Code=

	[[~~File~~::Main.java]]		[[Image::Main.java]]

	=Author=		=Author=

	* [[Jerome Avondo]]		* [[Jerome Avondo]]

JeromeAvondo at 13:24, 14 July 2010

2010-07-14T13:24:49Z

← Older revision		Revision as of 13:24, 14 July 2010
Line 48:		Line 48:
	=Source Code=		=Source Code=

	[[~~BioformatsConverters~~.java]]		[[File::Main.java]]

	=Author=		=Author=

	* [[Jerome Avondo]]		* [[Jerome Avondo]]

JeromeAvondo at 13:17, 14 July 2010

2010-07-14T13:17:00Z

← Older revision		Revision as of 13:17, 14 July 2010
Line 48:		Line 48:
	=Source Code=		=Source Code=

	~~link to SVN~~		[[BioformatsConverters.java]]

	=Author=		=Author=

	* [[Jerome Avondo]]		* [[Jerome Avondo]]

JeromeAvondo at 13:08, 2 June 2010

2010-06-02T13:08:13Z

← Older revision		Revision as of 13:08, 2 June 2010
Line 1:		Line 1:
			__NOTOC__
	[[Image:BioformatsConverterZip.png\|256px\|thumb]]		[[Image:BioformatsConverterZip.png\|256px\|thumb]]

			=Description=
	This software is useful for batch converting microscopy image formats, like STK, LSM, LIE, ZVI etc etc, to OME-TIFF or PNG files. See [http://www.loci.wisc.edu/ome/formats.html this page] for the supported image formats.		This software is useful for batch converting microscopy image formats, like STK, LSM, LIE, ZVI etc etc, to OME-TIFF or PNG files. See [http://www.loci.wisc.edu/ome/formats.html this page] for the supported image formats.
	The advantage of converting to OME-TIFF over regular TIFF files is that most of the original image metadata is kept in the file.		The advantage of converting to OME-TIFF over regular TIFF files is that most of the original image metadata is kept in the file.
Line 50:		Line 52:
	=Author=		=Author=

	* Jerome Avondo.		* [[Jerome Avondo]]

	~~__NOTOC__~~

JeromeAvondo at 13:20, 7 May 2010

2010-05-07T13:20:16Z

← Older revision		Revision as of 13:20, 7 May 2010
Line 47:		Line 47:

	link to SVN		link to SVN

			=Author=

			* Jerome Avondo.

	__NOTOC__		__NOTOC__