OMERO 4

• server stores Pixels files
• additionally, original files may be stored
• data duplication
• in triplicate for big images

OMERO 4

Getting Data In

OMERO 4

Getting Data In

• client software extracts planes from image files
• server stores and uses Pixels files
• Pixels files are uncompressed, so may be large
• additionally, original files could be archived
• data is duplicated

OMERO 4

Getting Data Out

OMERO 4

Getting Data Out

• clients obtain rendered images from server
• Pixels structure is optimized for reading
• rendering is thus a fast, direct process
• original files available only if archived

OMERO 5

• server does not store Pixels files
• only original files are stored
• no data duplication
• except for big images without subresolutions

OMERO 5

Getting Data In

OMERO 5

Getting Data In

• clients upload only the original files
• can disconnect after upload
• client and server compare files to check integrity
• no data duplication

OMERO 5

Getting Data Out

OMERO 5

Getting Data Out

• server now uses Bio-Formats in rendering
• Bio-Formats extracts planes from original files
• Bio-Formats performance much improved
• original files always available for download

Some Numbers

DV
(~125MB)

LEI
(~130MB / 140 TIFFs)

SVS
(~500MB)

InCell
(~9GB/~1000 TIFFs)

FS in Action #1

Importing and Downloading

We now show import and download in OMERO 5.

FS in Action #1

Importing and Downloading

• no archive checkbox
• file import is fast
• import log, aids debugging slow/failed
• checksums dialog for file integrity
• download files, content intact
• SVS viewable, uses subresolutions

No Data Duplication

• OMERO 5 does not create Pixels files
• no duplication of image data on server
• except for big images without subresolutions
• preserve original data structure
• uploaded image files readable by other software
• need not duplicate image data outside FS

More FS Advantages

• OMERO.server becomes master data repository
• easily share data, reproduce analyses
• protect against data loss on local systems
• each upload has an import log recorded
• Bio-Formats improvements benefit existing data

Introducing Filesets

• a set of related files
• Bio-Formats must read them together
• a set of images, arising from those files
• may be just one file and one image
• Project/Dataset, Screen/Plate hierarchy remains

One File → One Image

One File → Many Images

Many Files → Many Images

Many Files → One Image

• e.g. lei, metamorph?

Fileset Indivisibility

• files must be kept together for Bio-Formats
• must also associate the files' images
• server prohibits certain acts on partial filesets
• move between groups
• delete

FS in Action #2

Moving and Deleting

We now show move and delete in OMERO 5.

FS in Action #2

Moving and Deleting

• change group: partial fails
• change group: complete succeeds
• split fileset images across datasets
• delete: partial fails
• delete: complete succeeds

Migrating to FS

• new OMERO users should try out OMERO 5
• upgrades will be provided between each beta
• and to 5.0.0 and beyond
• upgrades from OMERO 4 currently being tested
• process for upgrade to be released after summer
• pre-FS data will be supported

Migrating to FS

Migrating to FS

Building on FS

• reconsider fileset handling (deletion, etc.)
• server-side recovery from partial deletes?
• detect and report post-upload file corruption

Next-Generation FS

Getting Data In

Next-Generation FS

Getting Data In

• import without Bio-Formats on clients
• all file format scanning done on server
• file upload from web client
• ability to upload unknown file formats

The Managed Repository

/home/data/sample$ tree zeiss-lsm-martin/  # Files local to client
zeiss-lsm-martin/
├── 01-01.lsm
├── 01-02.lsm
└── 051215-j-tf.mdb

            

/OMERO/ManagedRepository/josh_0$ tree .    # Files on the server
.
├── 2013-06
│   ├── 17
│   │   ├── 09-02-55.180
│   │   │   ├── 01-01.lsm
│   │   │   ├── 01-02.lsm
│   │   │   └── 051215-j-tf.mdb
│   │   ├── 09-02-55.180.log
            

Configuring FS

etc/omero.properties

• Managed Repository Directory

omero.data.dir=/OMERO/
omero.managed.dir=${omero.data.dir}/ManagedRepository

• Template Paths

omero.fs.repo.path=%user%_%userId%/%year%-%month%/%day%/%time%

Configuring FS

etc/omero.properties

Permitted File Naming

omero.fs.repo.path_rules=Windows required, UNIX required

Configuring FS

etc/omero.properties

Default Checksum Algorithm

omero.checksum.default=SHA1-160

FS in SQL

Find an Image's Fileset

SELECT fileset FROM image WHERE id = ?

FS in SQL

Find Images in Fileset

SELECT name FROM image WHERE fileset = ?

FS in SQL

Find Paths of Files in Fileset

SELECT of.path || of.name 
FROM originalfile of, filesetentry fse 
WHERE of.id = fse.originalfile 
AND fse.fileset = ?

FS in SQL

Find Checksums of Files in Fileset

SELECT of.name, ca.value, of.hash 
FROM originalfile of, filesetentry fse, checksumalgorithm ca 
WHERE of.hasher = ca.id 
AND of.id = fse.originalfile 
AND fse.fileset = ?