Human Embryology - User contributions [en]

DEC OMERO Server

2023-10-17T05:01:30Z

Admin:

[[File:Ome-logo-400.png|300px|link=https://www.openmicroscopy.org]]
==About the Collection Server==
[[File:OmeroWeb.png|thumb|alt=OmeroWeb|OmeroWeb]]
 
{{OMEROlink}}
 
{|
! Image Server Update - Feb 2020
|-
| We are currently updating server version to OMERO 5.5.1 Image server may be unavailable during this process.

|}
 
{|
! Image Server Update - June 2019
|-
| We are currently updating server version to OMERO 5.5. Image server may be unavailable during this process.

A standard OMERO user just needs to download the client package with the same major version as their institutional server (e.g. 5.3.0 clients will connect to 5.3.5 servers but not to 5.4.0 servers). Full instructions for installation are on the help site.
|}
 
{|
! Image Server Update - January 2019
|-
| [[User:MarkHill|MarkHill]] ([[User talk:MarkHill|talk]]) 11:11, 29 January 2019 (AEDT) Power failure in University shutdown server. We are checking database before restarting DEC server.
|-
| January 2019 - DEC Server upgraded (OMERO 5.4.9), tested and back online.

[[User:MarkHill|MarkHill]] ([[User talk:MarkHill|talk]]) 14:06, 16 January 2019 (AEDT)
|}

{|
! Image Server Update - Oct 2017
|-
| Dear DEC Users - Software has been updated to Omero Server (version 5.4). You will be able to access the database with your web browser as before.

To upload new images you will need to download and install the latest version of [https://www.openmicroscopy.org/omero/downloads/ OMERO.Insight] (5.4.0).

[[User:MarkHill|MarkHill]] ([[User talk:MarkHill|talk]]) 12:07, 11 October 2017 (AEDT)
|}

{|
! Image Server Update - Apr 2017
|-
| Dear DEC Users - Software is currently being updated to Omero Server (version 5.3, [https://www.openmicroscopy.org/community/viewtopic.php?f=11&t=8254 announcement]). During this period there will be numerous times that the image server will be unavailable. I apologise for any inconvenience. I will be sending an email to all users when installation and testing has been completed.

[https://www.openmicroscopy.org/community/viewtopic.php?f=11&t=8254 OMERO 5.3 release] - [http://glencoesoftware.com/2016-08-30-glencoe-software-zeiss-partner-open-source-file-reader-whole-slide.html JPGXR announcement]

[[User:MarkHill|MarkHill]] ([[User talk:MarkHill|talk]]) 10:24, 21 April 2017 (AEST)
|}

The collection scanned images are currently available as a test site with only a few sample images loaded. There is no unregistered user access available to the server. All users must apply for an account and agree to abide by our access and reuse conditions before being issued a user account. Individual user accounts currently only have access to specific folders. Access to other collection folders can be managed through user rights management.

:[[Help|'''User Help''']] - [[Help#OMERO_Image_Server_Log_In|Image Server Log in]]  |   [[Help#DEC_Log_In|DEC Log in]]

For server issues, access problems or account requests, please contact [mailto:m.hill@unsw.edu.au?Subject=DEC%20OMERO%20Server%20Request Dr Mark Hill].

{{OMEROlink}}

[[File:DEC image server pie 30Jun2017.jpg|thumb|DEC Image database (Jun2017)]]

Collections have been organised into folders named approximately after the original collection name or location.

==Apply for DEC Account==
For DEC user account requests, please contact [mailto:m.hill@unsw.edu.au?Subject=Apply%20for%20DEC%20account Dr Mark Hill].

Agreement to the following "terms of use" are required either in writing or by email using your official institutional letterhead or email address and signature. Please make special note of conditions 1 and 2 concerning image reuse. Failure to comply with the "terms of use" will result in immediate suspension of user account database access without notice.

===Terms of Use===

By using the DEC OMERO Server, you agree to the following:

# You agree to the specific conditions set by each collections terms of image reuse, publication and copyright.
# Reuse of images from multiple collections requires approval from each collection.
# You use this service at your own risk, and we provide NO GUARANTEE OR WARRANTY WHATSOEVER regarding uptime, security, data provenance or access, or any other service.
# You should not use the DEC OMERO Server as a repository for any important data, or data that must be held in any secure or specific way.
# The responsibility for any data loaded onto the DEC OMERO Server is entirely your own.
# We reserve the right to remove any images, data, accounts or other data or structure without notice or request.
# We welcome comments or ideas from your use of and experience with the DEC OMERO Server.

==OMERO Image Server Log In==
{|
| valign=top|'''Only registered users can log in and edit the OMERO website.'''
# Click on image server (menu at top of each page).
# This opens the DEC Omero Server information page.
# Click on the text link "DEC Omero Server"
# Log in screen then opens, fill in your "User Name" and "Password" (supplied by email).
# Click "Login", will open the database in your user view.
# Access projects and images in the folders shown on the left.
# Access your user information at the top righthand corner.
 
|-
| '''The animation below shows the above text described process.'''
 
|}
===OMERO Training Manual===

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.

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|Manual PDF]]

===2017 Test Image Link===
This only in a trial, final database will vary from this draft structure.

* '''Folder''' - Each embryo has own folder (with the original embryo name as it exists in your collection).
* '''Project Details''' - CRL in mm and total number of slides available (from catalogue).
* '''Tag''' - Plane of embryo section (Sagittal, Frontal, Transverse).

====July====
Locally uploaded image samples.

* Blechschmidt Collection in Christop Viebahn folder http://149.171.80.223:8080/webclient/?show=dataset-641
* Hinrichsen Collection in Beate Brand-Saberi folder http://149.171.80.223:8080/webclient/?show=dataset-735
* Hubrecht Collection in Peter Giere folder http://149.171.80.223:8080/webclient/?show=dataset-786

====June====
[[DEC OMERO Server|Selected slides]] form the [[Blechschmidt Collection]] are available for registered user access. Please advise me if you are unable to see the linked files below following log-in.

* 2.57 mm sagittal - 22 slides total 23 ([http://149.171.80.223:8080/webclient/?show=project-253 '''1954-08-10'''])
* 3.4 mm sagittal - 82 slides total 87 ([http://149.171.80.223:8080/webclient/?show=project-255 '''1954-04-09'''])
* 4 mm sagittal - 3 slides total 4 ([http://149.171.80.223:8080/webclient/?show=project-262 '''1951-05-05'''])
* 5.8 mm frontal - 54 slides total 77 ([http://149.171.80.223:8080/webclient/?show=project-252 '''1954-09-20'''])
* 6.5 mm sagittal - 40 slides total 40 ([http://149.171.80.223:8080/webclient/?show=project-258 '''1953-09-29'''])
* 11 mm frontal - 29 slides total 76 ([http://149.171.80.223:8080/webclient/?show=project-261 '''1951-09-01'''])

==About OMERO==

[https://www.openmicroscopy.org/site OMERO] is client-server software for visualization, management and analysis of biological microscope images. © 2000-2016 University of Dundee & Open Microscopy Environment. [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License] OME source code is available under the GNU General public license or through commercial license from Glencoe Software.

Version - OMERO.web 5.0.8-ice35.

==Software Download==
Dear DEC Users - Log below shows currently updated Omero Server software version.

* Jan 2019 - Software to Omero Server (version 5.4.10)
* Oct 2017 - Software to Omero Server (version 5.4, [https://www.openmicroscopy.org/2017/10/09/omero-5-4-0.html announcement]).
* 2016 - [https://www.openmicroscopy.org/community/viewtopic.php?f=11&t=8254 OMERO 5.3 release] - [http://glencoesoftware.com/2016-08-30-glencoe-software-zeiss-partner-open-source-file-reader-whole-slide.html JPGXR announcement]

===Image Uploader/Insight Software===
OMERO Server has recently been updated to version 5.4 ([https://www.openmicroscopy.org/2017/10/09/omero-5-4-0.html announcement]). The associated software suite has also been updated to this new version and should be used to upload your image files. Use the links below to download and install from the original source.

'''Download Page'''
* [https://www.openmicroscopy.org/omero/downloads/OMERO 5.4]

==References==

{{#pmid:31579322}}

{{#pmid:30377375}}

{{#pmid:28775673}}

{{#pmid:22373911}}

{{#pmid:20513764}}

==Links==
* [https://www.openmicroscopy.org/site The Open Microscopy Environment]
* [https://www.openmicroscopy.org/omero/ OMERO 5.4 Download]
* [https://www.openmicroscopy.org/2020/07/16/omero-5-6-2.html OMERO 5.6.2 Download]
* [http://help.openmicroscopy.org OME Help]
* [http://help.openmicroscopy.org/web-client.html Using OMERO.web]
* [http://help.openmicroscopy.org/resources.html Training Course Manual]
* [http://help.openmicroscopy.org/importing-data-5.html Importing Data with OMERO.insight Version 5]
* [http://jcb-dataviewer.rupress.org JCB DataViewer]
* [https://imagej.net/Fiji/Downloads Fiji] (ImageJ)
* [https://www.openmicroscopy.org/site/support/bio-formats5.5/supported-formats.html Image formats]

{{Footer}}

Help

2023-10-17T05:00:51Z

Admin:

==Introduction==
This resource, human-embryology.org, is the website of the Digital Embryology Consortium.
This page will eventually contain help information about using the site and accessing the image database.

{{Draft page}}

==DEC Log In==
{|
| valign=top|'''Only registered users can log in and edit the DEC website.'''
# Click on the small grey head profile (upper righthand corner).
# Select "Log in" from the dropdown menu.
# Log in screen then opens, fill in your "User Name" and "Password" (supplied by email).
# Click "Log in", will return to the original page (small head profile is now blue)
# Access your own page by clicking the head profile and selecting your name from the dropdown menu.

Note - the same "User Name" and "Password" are used to access to the [http://149.171.80.223:8080/webclient/login/?url=%2Fwebclient%2F image database].
| '''This animation shows the described process.'''

|}

==OMERO Image Server Log In==
{|
| valign=top|'''Only registered users can log in and edit the OMERO website.'''
# Click on image server (menu at top of each page).
# This opens the DEC Omero Server information page.
# Click on the text link "DEC Omero Server"
# Log in screen then opens, fill in your "User Name" and "Password" (supplied by email).
# Click "Login", will open the database in your user view.
# Access projects and images in the folders shown on the left.
# Access your user information at the top righthand corner.

Note - the same "User Name" and "Password" are used to access to the [[Main Page|DEC website]].
| '''This animation shows the described process.'''
|}

==Interlanguage Links==
Currently only the main page is available in a variety of [[Languages|languages]]. These are accessed by the flag links at the bottom of the main page and shown below.

Link: [[Languages]]

{|
! colspan=2|Translate this page
|-
| width="90px" valign=top|<center>[[File:Australia_flag.png|60px|link=human-embryology.org]]</center>
| width="90px" valign=top|<center>[[File:German_flag.png|60px|link=De:Human-embryology.org]]</center>
| width="90px" valign=top|<center>[[File:Spain_flag.png|60px|link=Es:Human-embryology.org]]</center>
| width="90px" valign=top|<center>[[File:Canada flag.png|60px|link=Fr:Human-embryology.org]]</center>
| width="90px" valign=top|<center>[[File:Japan_flag.png|60px|link=Jp:Human-embryology.org]]</center>
|
{| class="wikitable mw-collapsible mw-collapsed"
! colspan=2|Other Languages 
|-
| [[Eg:Human-embryology.org|Arabic (العربية)]] | [[Cn:Human-embryology.org|Chinese (中文)]] | [[Il:Human-embryology.org|Hebrew (עִברִית)]] | [[In:Human-embryology.org|Hindi (भारतीय)]] | [[Id:Human-embryology.org|Indonesian (bahasa Indonesia)]] | [[It:Human-embryology.org|Italian (Italiano)]] | [[Kr:Human-embryology.org|Korean (한국어)]] | [[Br:Human-embryology.org|Portuguese (português)]] | [[Ru:Human-embryology.org|Russian (русский)]] | [[Pk:Human-embryology.org|Urdu (اردو)]]
|}
|-
| valign=top|<center>English</center>
| valign=top|<center>Deutsch</center>
| valign=top|<center>[[Es:Human-embryology.org|Español]]/[[Cat:Human-embryology.org|Català]]</center>
| valign=top|<center>Français</center>
| valign=top|<center>日本人</center>
|
|}

===Adding content in another language===
If you intend to add content to the Wiki in a language, other than English, please use the 2 letter language code in front of the page name. This list is based upon the current contributing collections. See also the page [[Languages]].

{|
|-bgcolor="CEDFF2"
! width=150px|Language
! 2 letter Code
|-
| English || no code letter
|-
| German || De:
|-
| Spanish || Es:
|-
| French || Fr:
|-
| Japanese || Jp:
|}

This site does not use the Wiki [https://en.wikipedia.org/wiki/Help:Interlanguage_links Interlanguage links] solution.

https://translate.google.com.au/

==Wiki Code Shortcuts==

===Semantics===
[[User:MarkHill|MarkHill]] ([[User talk:MarkHill|talk]]) 10:44, 30 October 2018 (AEDT) [[Semantic MediaWiki]] has now been disabled with the current Wiki software update.

===Page Templates===

* <nowiki>{{Footer}}</nowiki> - Currently just shows common pages on site but can be used for anything that you want to appear on all pages. Added at the bottom of pages.
* <nowiki>{{Draft page}}</nowiki> - Added to pages that are incomplete or placeholders until content added. This notice should be removed when the page is considered completed.

===Useful Code===

{| class="wikitable mw-collapsible mw-collapsed"
! Collapsible Table 
|-
| The   moves the Expand//Collapse button away from the text.
|}

{|
|-bgcolor="Yellow"
| Yellow
| Yellow
|-bgcolor="LightYellow"
| LightYellow
| LightYellow
|-bgcolor="FAF5FF"
| text
| "FAF5FF"
|-bgcolor="a3bfb1"
| dark green
| "A3BFB1"
|-bgcolor="F5FFFA"
| light green
| "F5FFFA"
|-bgcolor="FCFCFC"
| light grey
| "FCFCFC"
|-bgcolor="FCFCFC"
| light grey
| "FCFCFC"
|-bgcolor="F5FAFF"
| light blue
| "F5FAFF"
|-bgcolor="CEDFF2"
| dark blue
| "CEDFF2"
|-bgcolor="DDCEF2"
| dark purple
| "DDCEF2"
|-bgcolor="FAF5FF"
| light purple
| "FAF5FF"
|-bgcolor="FFCC00"
| yellow
| "FFCC00"
|}

===Insert YouTube Video===
Set the size you wish to appear on the page and use the 13 character code for the video. [[:File:Owncloud-logo.png|Here is an example on this site]].

{{Footer}}

Test page

2023-10-03T04:08:46Z

Admin:

{{De-Header}}
==Test page - Testseite==
{|
|-bgcolor=Yellow
! English
! German
|-
| A page for drafting content or testing formatting.
| Eine Seite für die Ausarbeitung der Inhalte oder Test Formatierung.
|-bgcolor=LightYellow
| Permitted upload file types: doc, mov, mp4, m4v, pdf, ogg, flv, swf, jpg, jpeg, png, gif, pptx, ppt, mp3, xls, psd, jp2, tif.
| Zulässige Upload-Dateitypen: : doc, mov, mp4, m4v, pdf, ogg, flv, swf, jpg, jpeg, png, gif, pptx, ppt, mp3, xls, psd, jp2, tif.
|-
|
|}

2023/10/03

{{Footer}}
{{De-Footer}}

User:Admin

2023-08-05T10:18:11Z

Admin:

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User:Admin

2023-08-05T10:17:29Z

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2018-11-28T00:48:39Z

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2018-11-28T00:48:01Z

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Richard Test

2017-11-22T02:20:33Z

Admin:

This is a test page created Wed Nov 22 13:09:35 AEDT 2017

This is an edit on the test page made at Wed Nov 22 13:09:35 AEDT 2017

This is another edit on the page https://human-embryology.org/index.php?title=Richard_Test made a bit later at Wed Nov 22 13:17:53 AEDT 2017

Another edit. This one at Wed Nov 22 13:20:21 AEDT 2017

Richard Test

2017-11-22T02:18:06Z

Admin:

Richard Test

2017-11-22T02:10:39Z

Admin:

This is a test page created Wed Nov 22 13:09:35 AEDT 2017

This is an edit on the test page made at Wed Nov 22 13:09:35 AEDT 2017

Richard Test

2017-11-22T02:09:55Z

Admin: This is a test page

This is a test page created Wed Nov 22 13:09:35 AEDT 2017