DEC Online Database - Revision history

MarkHill: /* JPEG 2000 */

2018-11-05T00:05:33Z

JPEG 2000

← Older revision		Revision as of 10:05, 5 November 2018
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	* Part 1 giving (mostly) codec information (how to compress/decompress image data), with a container file format annex (JP2).		* Part 1 giving (mostly) codec information (how to compress/decompress image data), with a container file format annex (JP2).
	* Part 2 gives many extensions, and a more comprehensive container format (JPX).		* Part 2 gives many extensions, and a more comprehensive container format (JPX).


			* Zeiss JPEG-XR cannot be ported to the Olympus files without major work.

	==Apply for DEC Account==		==Apply for DEC Account==

MarkHill: /* About the Online Database */

2017-11-30T02:07:00Z

About the Online Database

← Older revision		Revision as of 12:07, 30 November 2017
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	Database Images:		Database Images:
			* can be accessed and downloaded remotely through any web browser link to [http://149.171.80.223 DEC Database].
	* can be imported, accessed and downloaded remotely through OMERO.insight or ImageJ/Fiji.		* can be imported, accessed and downloaded remotely through OMERO.insight or ImageJ/Fiji.
	* can be accessed and downloaded remotely through any web browser link to [http://149.171.80.223 DEC Database].

	==Importing Data==		==Importing Data==
	The two methods for importing data are shown below.		The two methods for importing data are shown below.

MarkHill: /* ImageJ/Fiji */

2017-11-30T02:05:53Z

ImageJ/Fiji

← Older revision		Revision as of 12:05, 30 November 2017
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	# Add the required plug-ins.		# Add the required plug-ins.
	# Log into the database through the OMERO plug-in.		# Log into the database through the OMERO plug-in.






	Original Video Links		Original Video Links
	* [https://downloads.openmicroscopy.org/movies/omero-5-2/mov/fiji_omero_manual_workflow.mov Fiji-OMERO workflow]		* [https://downloads.openmicroscopy.org/movies/omero-5-2/mov/fiji_omero_manual_workflow.mov Fiji-OMERO workflow]
	* [https://downloads.openmicroscopy.org/movies/omero-5-2/mov/fiji_scripting_demo.mov Scripting with Fiji and OMERO]		* [https://downloads.openmicroscopy.org/movies/omero-5-2/mov/fiji_scripting_demo.mov Scripting with Fiji and OMERO]


	\| <html5media width="500" height="400">File:Fiji omero manual workflow 2016.mp4</html5media>		\| <html5media width="500" height="400">File:Fiji omero manual workflow 2016.mp4</html5media>
	\|}		\|}

MarkHill at 02:03, 30 November 2017

2017-11-30T02:03:21Z

← Older revision		Revision as of 12:03, 30 November 2017
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	==Importing Data==		==Importing Data==
	===1. OMERO.insight===		The two methods for importing data are shown below.

			===OMERO.insight===
	Images are added to the database by the process called "Importing Data" using the software [http://help.openmicroscopy.org/importing-data-5.html OMERO.insight Version 5]. Please read the [[Media:DEC-OMERO-training-manual-2017.pdf\|'''DEC OMERO training manual''']] before uploading images to the test version of the image server.		Images are added to the database by the process called "Importing Data" using the software [http://help.openmicroscopy.org/importing-data-5.html OMERO.insight Version 5]. Please read the [[Media:DEC-OMERO-training-manual-2017.pdf\|'''DEC OMERO training manual''']] before uploading images to the test version of the image server.

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	20 July 2017 - Please note error on Page 4 of training manual the server address to enter should be '''149.171.80.223''' not the full web address shown in the original manual (http://149.171.80.223:8080). My apologies for this error.		20 July 2017 - Please note error on Page 4 of training manual the server address to enter should be '''149.171.80.223''' not the full web address shown in the original manual (http://149.171.80.223:8080). My apologies for this error.

	===2. ImageJ/Fiji===		===ImageJ/Fiji===

	Images can also be added to the database as well as adding ROI's to existing images through ImageJ/Fiji. I am currently preparing a DEC manual and video to demonstrate this process. Best place to currently begin using ImageJ/Fiji is with the original OMERO help page [http://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] and the 2016 demonstration video below.		Images can also be added to the database as well as adding ROI's to existing images through ImageJ/Fiji. I am currently preparing a DEC manual and video to demonstrate this process. Best place to currently begin using ImageJ/Fiji is with the original OMERO help page [http://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] and the 2016 demonstration video below.
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	# Add the required plug-ins.		# Add the required plug-ins.
	# Log into the database through the OMERO plug-in.		# Log into the database through the OMERO plug-in.

			Original Video Links
			* [https://downloads.openmicroscopy.org/movies/omero-5-2/mov/fiji_omero_manual_workflow.mov Fiji-OMERO workflow]
			* [https://downloads.openmicroscopy.org/movies/omero-5-2/mov/fiji_scripting_demo.mov Scripting with Fiji and OMERO]


	\| <html5media width="500" height="400">File:Fiji omero manual workflow 2016.mp4</html5media>		\| <html5media width="500" height="400">File:Fiji omero manual workflow 2016.mp4</html5media>
	\|}		\|}

MarkHill: /* OMERO Videos */

2017-11-30T02:00:54Z

OMERO Videos

← Older revision		Revision as of 12:00, 30 November 2017
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	\| <html5media width="500" height="400">File:Fiji omero manual workflow 2016.mp4</html5media>		\| <html5media width="500" height="400">File:Fiji omero manual workflow 2016.mp4</html5media>
	\|}		\|}

	~~===OMERO Videos===~~
	* [https://downloads.openmicroscopy.org/movies/omero-5-2/mov/fiji_omero_manual_workflow.mov Fiji-OMERO workflow]
	* [https://downloads.openmicroscopy.org/movies/omero-5-2/mov/fiji_scripting_demo.mov Scripting with Fiji and OMERO]

	==Collections==		==Collections==

MarkHill: /* 2. ImageJ/Fiji */

2017-11-30T02:00:02Z

2. ImageJ/Fiji

← Older revision		Revision as of 12:00, 30 November 2017
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	Images can also be added to the database as well as adding ROI's to existing images through ImageJ/Fiji. I am currently preparing a DEC manual and video to demonstrate this process. Best place to currently begin using ImageJ/Fiji is with the original OMERO help page [http://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] and the 2016 demonstration video below.		Images can also be added to the database as well as adding ROI's to existing images through ImageJ/Fiji. I am currently preparing a DEC manual and video to demonstrate this process. Best place to currently begin using ImageJ/Fiji is with the original OMERO help page [http://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] and the 2016 demonstration video below.

			{\|
			\|
	# Install ImageJ/Fiji.		# Install ImageJ/Fiji.
	# Add the required plug-ins.		# Add the required plug-ins.
	# Log into the database through the OMERO plug-in.		# Log into the database through the OMERO plug-in.
			\| <html5media width="500" height="400">File:Fiji omero manual workflow 2016.mp4</html5media>
			\|}

	===OMERO Videos===		===OMERO Videos===

MarkHill: /* 2. ImageJ/Fiji */

2017-11-30T01:57:48Z

2. ImageJ/Fiji

← Older revision		Revision as of 11:57, 30 November 2017
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	===2. ImageJ/Fiji===		===2. ImageJ/Fiji===

	Images can also be added to the database as well as adding ROI's to existing images through ImageJ/Fiji. I am currently preparing a DEC manual and video to demonstrate this process. Best place to currently begin using ImageJ/Fiji is with the original OMERO help page [http://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] and the demonstration video below.		Images can also be added to the database as well as adding ROI's to existing images through ImageJ/Fiji. I am currently preparing a DEC manual and video to demonstrate this process. Best place to currently begin using ImageJ/Fiji is with the original OMERO help page [http://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] and the 2016 demonstration video below.


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	# Add the required plug-ins.		# Add the required plug-ins.
	# Log into the database through the OMERO plug-in.		# Log into the database through the OMERO plug-in.





	===OMERO Videos===		===OMERO Videos===

MarkHill: /* 2. ImageJ/Fiji */

2017-11-30T01:56:51Z

2. ImageJ/Fiji

← Older revision		Revision as of 11:56, 30 November 2017
Line 27:		Line 27:
	===2. ImageJ/Fiji===		===2. ImageJ/Fiji===

	Images can also be added to the database as well as adding ROI's to existing images through ImageJ/Fiji. I am currently preparing a DEC manual and video to demonstrate this process.		Images can also be added to the database as well as adding ROI's to existing images through ImageJ/Fiji. I am currently preparing a DEC manual and video to demonstrate this process. Best place to currently begin using ImageJ/Fiji is with the original OMERO help page [http://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO] and the demonstration video below.


	# Install ImageJ/Fiji.		# Install ImageJ/Fiji.
	# Add the required plug-ins.		# Add the required plug-ins.
	# Log into the database through the OMERO plug-in.		# Log into the database through the OMERO plug-in.





			===OMERO Videos===
			* [https://downloads.openmicroscopy.org/movies/omero-5-2/mov/fiji_omero_manual_workflow.mov Fiji-OMERO workflow]
			* [https://downloads.openmicroscopy.org/movies/omero-5-2/mov/fiji_scripting_demo.mov Scripting with Fiji and OMERO]

	==Collections==		==Collections==

MarkHill: /* ImageJ/Fiji with OMERO */

2017-11-30T01:55:32Z

ImageJ/Fiji with OMERO

← Older revision		Revision as of 11:55, 30 November 2017
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	File:Test image20160330-3.jpg\|Spinal cord central canal		File:Test image20160330-3.jpg\|Spinal cord central canal
	</gallery>		</gallery>

	~~==ImageJ/Fiji with OMERO==~~

	~~Best place to begin using ImageJ/Fiji is with the original external help page - [http://help.openmicroscopy.org/imagej.html Using ImageJ with OMERO].~~

	~~===OMERO Videos===~~

	* [https://downloads.openmicroscopy.org/movies/omero-5-2/mov/fiji_omero_manual_workflow.mov Fiji-OMERO workflow]
	* [https://downloads.openmicroscopy.org/movies/omero-5-2/mov/fiji_scripting_demo.mov Scripting with Fiji and OMERO]

	==Image Formats==		==Image Formats==

MarkHill: /* 1. OMERO.insight */

2017-11-30T01:54:07Z

1. OMERO.insight

← Older revision		Revision as of 11:54, 30 November 2017
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	==Importing Data==		==Importing Data==
	===1. OMERO.insight===		===1. OMERO.insight===
	Images are added to the database by the process called "Importing Data" using the software [http://help.openmicroscopy.org/importing-data-5.html OMERO.insight Version 5]		Images are added to the database by the process called "Importing Data" using the software [http://help.openmicroscopy.org/importing-data-5.html OMERO.insight Version 5]. Please read the [[Media:DEC-OMERO-training-manual-2017.pdf\|'''DEC OMERO training manual''']] before uploading images to the test version of the image server.


	* [[Media:DEC-OMERO-training-manual-2017.pdf\|DEC OMERO Training Manual (PDF)]]		* [[Media:DEC-OMERO-training-manual-2017.pdf\|DEC OMERO Training Manual (PDF)]]
	* Help - [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight Version 5]		* Help - [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight Version 5]


			20 July 2017 - Please note error on Page 4 of training manual the server address to enter should be '''149.171.80.223''' not the full web address shown in the original manual (http://149.171.80.223:8080). My apologies for this error.

	===2. ImageJ/Fiji===		===2. ImageJ/Fiji===