Talk:DEC OMERO Server

From Human Embryology

2019

http://149.171.80.223:8080/webclient/login/?url=%2Fwebclient%2F


2017

Issues

  • Non-scrolling lefthand window.
    • Means that long lists of files need to be manually stepped through
    • Menu at bottom of this window also does not display correctly when scrolling long file list.
  • Tags cannot be moved between collection groups.
    • The entire Tag Set and Tag list has to be added individually to each collection.


Tags

These are new tags added to the online database. Some relate to whole embryo and some are for individual slides.

Currently "Tags" cannot be moved between collection groups. In order to add the entire Tag Set and Tag list has to be added individually to each collection.

Collection

  • Blechschmidt - (whole embryo) Should act as Gottingen collection identifier tag when searching whole library.
  • Hindrichsen - (whole embryo) Should act as Bochum collection identifier tag when searching whole library.

Plane

  • Sagittal - (whole embryo) plane dividing the body into left and right halves.
  • Transverse - (whole embryo)
  • Frontal - (whole embryo)

Histology

Note - Some embryos have 2 to 3 different stains used in the serial sections. Too difficult at this stage to tag each slide so currently (whole embryo) may be tagged with multiple stains.

  • Toluidine Blue - (whole embryo) Histology stain, nucleus blue and cytoplasm light blue. (Example - Hindrichsen ME65 heart)

Housekeeping

Related to database activities. Should allow easy identification of upload fails.

  • Fail - (individual slide) added to individual slides that fail to upload with OMERO.insight (Example - Hindrichsen Embryo 283 slides 478-484, Embryo 335 slides 160-164)

OMERO 5.3

17 March 2017

1. open up terminal

2. start postgresql pg_ctl -D /usr/local/var/postgres -l /usr/local/var/postgres/server.log -w start

3. start omero admin omero admin start

4. start omero web omero web start

5. start nginx nginx -c $(brew --prefix omero53)/etc/nginx.conf

6. you can now access OMERO through: http://149.171.80.223:8080/

References

Melissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology, Vol. 189no. 5777-782 doi: 10.1083/jcb.201004104 PMID 20513764

Chris Allan, Jean-Marie Burel, Josh Moore, Colin Blackburn, Melissa Linkert, Scott Loynton, Donald MacDonald, William J Moore, Carlos Neves, Andrew Patterson, Michael Porter, Aleksandra Tarkowska, Brian Loranger, Jerome Avondo, Ingvar Lagerstedt, Luca Lianas, Simone Leo, Katherine Hands, Ron T Hay, Ardan Patwardhan, Christoph Best, Gerard J Kleywegt, Gianluigi Zanetti & Jason R Swedlow (2012) OMERO: flexible, model-driven data management for experimental biology. Nature Methods 9, 245–253. Published: 28 February 2012 PMID 22373911

Image Data Resource (IDR) http://idr-demo.openmicroscopy.org/about/index.html

OMERO.mapr. https://github.com/ome/omero-mapr/tree/master/docs

OpenStack https://www.openstack.org/software/start/

OMERO 5.2

OMERO.server installation on OS X with Homebrew

This documentation is for OMERO 5.2. This version is now in maintenance mode and will only be updated in the event of critical bugs or security concerns.


OMERO 5.3 - JPGXR announcement

Chris Allan - Software Engineer callan@glencoesoftware.com


Install Instructions

2016

Release of OMERO 5.2.7

Postby jburel » Tue Dec 13, 2016 12:05 pm

Dear All,

Today we are releasing OMERO 5.2.7. This is a release aimed at system administrators or developers wanting to build OMERO with Ice 3.6.3.

This release also upgrades the version of Bio-Formats which OMERO uses to 5.1.10 [1].

All scripts handling Regions of Interest (ROIs) now support ROI not linked to any plane as defined by the OME Model.

The software is available at: http://downloads.openmicroscopy.org/omero/5.2.7

Regards,

The OME Team


June 2015 Meeting

https://www.openmicroscopy.org/site/community/minutes/meetings/10th-annual-users-meeting-june-2015

Test Image Link

Sydney folder -> 2010-08-29-1 -> Stage 22 Human Embryo (Mark Hill-001.svs) dimensions 32538 x 28770

(Note - Will need to login to access image)

Server Groups

  • Private (rw----): All data in this group is only visible to the user who owns it and the group owner. Other users cannot see who else is in the group or view their data. The group owner can view the data for other group members but not make any edits (same as read-only behaviour).
  • Read-Only (rwr---): Users in groups with this permission setting can view each others' data, but cannot edit or annotate another user's data. You can view another users' images but not comment, rate or tag their images.
  • Read-Annotate (rwra--): Users in a Read-Annotate group can view and annotate the data belonging to other users. You can tag another user's images or use their tags to annotate your own images. You can add comments to their images and save your own rendering settings for each image. However, you cannot edit the names of their images, projects, datasets or tags etc.

Hardware

Apple

  • Model Name - Mac Pro (Late 2013)
  • Model Identifier - MacPro6,1
  • Processor Name - Quad-Core Intel Xeon E5
  • Processor Speed - 3.7 GHz
  • Number of Processors - 1
  • Total Number of Cores - 4
  • L2 Cache (per Core) - 256 KB
  • L3 Cache - 10 MB
  • Memory - 12 GB
  • Thunderbolt - Apple’s Thunderbolt 2 can support up to six devices in a daisy chain, on a single port.

Storage

Areca ARC-5028T2, Thunderbolt 2, 6 Gb/s, 6-Bay

  • features two interfaces, Thunderbolt 2 and SuperSpeed USB 3.0. Thunderbolt 2 pushes performance up to 20Gbs and enables 4K video file transfer and display simultaneously. The ARC-5028T2 is equipped with dual Thunderbolt 2 ports for connecting to any Thunderbolt 2 enabled host such as the new Mac Pro, and is backwards compatible to the same cables and connectors used with current Thunderbolt devices. In addition to high performance Thunderbolt 2, the ARC-5028T2 also gives the user the option to connect by SuperSpeed USB 3.0 interface for environments not having a Thunderbolt port.
  • File:ARC 5028T2 Quick Start Guide.pdf
  • File System - Journaled HFS+

HDD

  • Seagate (7200 RPM) 8Tb, 128 Mb cache, SATA 3, 6Gb/s (ST8000AS0002-1NA17Z)
  • HGST Deskstar NAS (7200 RPM) 4Tb, 64 Mb cache, SATA 3, 6 Gb/s

RAID

The DEC storage device uses a RAID 5 (Redundant Array of Inexpensive Disks 5) configuration.

  • RAID 0 – Fast, cheap, no data redundancy. Requires a minimum of two hard drives inside the RAID enclosure. Most often used when speed combined with low cost are paramount.
  • RAID 1 – Complete data redundancy. Requires a minimum of two hard drives inside the RAID enclosure. Often called “mirroring,” each drive is a complete copy of the other. Most often used for backing up servers or when on-set for DIT media work. No faster than the slowest drive in the system.
  • RAID 3 – Very fast, data redundancy. Requires a minimum of three drives. More popular on the PC than the Mac. Should one drive go down, your data is safe. This technology has been principally replaced by RAID 5 systems.
  • RAID 5 – Very fast, data redundancy. Requires a minimum of three drives. Most often found with four or five drives inside. More popular on the Mac, when one drive goes down, your data is safe. This is the most popular mid-priced RAID for video editing and generally connected to just one computer system.
  • RAID 6 – Fast, extra data redundancy. Requires a minimum of four drives. This version protects your data in the event two hard drives die at the same time. More expensive than RAID 5, but, generally, the same physical size. Like the RAID 5 this is most often used connected to just one computer. Not as fast as a RAID 5.

Space

2017

May 2016

  • Total usage: 48.19 GB
  • Free space: 36.33 TB

March 2016

  • Total usage: 48.19 GB
  • Free space: 18.14 TB


2016

Test Image Link (now disabled)

Note - You will need to login to access the original image through the links, images appearing on this current page are only screenshots.

Sydney folder -> 2010-08-29-1 -> Stage 22 Human Embryo (Mark Hill-001.svs) dimensions 32538 x 28770