Movie - Showcase OMERO script

[saloynton]

Script - version 2 - 12-08-10


Introduce OMERO

Explain OME - OMERO

Emphasise open-source open-standard

Showcase Bioformats - range of supported formats and constant updating

Mention can be used to collaborate

Show viewing of images and rendering settings

Draw ROIs and show analysis

Illustrate export options

Mention works with other apps like ImageJ and Matlab


Welcome to OMERO.

OMERO is part of the Open Microscopy Environment, an open-source project which produces tools to support data management for biological light microscopy and also for other imaging applications.

(Logo and zooming images)


OMERO clients run on your computer and connect to a central server run by your institution which stores and manages your image data. OMERO is fully cross-platform, with clients and servers running on Windows, Mac and Linux platforms.

(View and then zoom of overview/architecture image)


OMERO allows you to import image data from local and networked drives and store them in a central server. The import includes the metadata such as the microscope settings associated with the images. Image data is stored in the open-standard OME-TIFF format, and copies of the data in it's original format can be archived at the time of import.

(Speeded up sequence of data manager, importing images, showing data tree


OMERO uses the Bioformats engine to import over 120 image data formats including their metadata such as the acquisition data associated with the images. The list of supported formats is constantly updated and expanded.

(Shot scrolling down supported formats table from Bioformats website)


Images and their metadata are stored on the OMERO server in the open-standard OME-TIFF format. The original metadata imported with the image, such as the name of the microscope and its settings, is preserved and any further data added or changes made to the image rendering settings in OMERO are stored separately. OMERO also allows archiving of imported images in the original data format.

(Sequence of image viewer with metadata panel showing, demonstrating acquisition data and toggling of channels)


You can use OMERO to collaborate with colleagues, creating groups allowing data to be shared with and viewed by your co-workers.

(Sequence of adding groups to the data tree)


The image viewer allows you zoom into images, scroll across them and adjust rendering settings and channel colour assignments.

(Open image viewer and zoom, scroll across image, toggle off channel, change colour of channel)


Z- and t-stacks can be navigated through.

(Step through Z-stack and then play through it, play through time stack)


Regions of Interest can be drawn on images and analysis done on these regions. The ROIs are easily applied to all images in a dataset.

(Draw line ROI and ellipse ROI, show intensity measurements along line, apply ROIs across dataset)


Images can be output as figures for publication or movies by running scripts on selected images. And results of analysis can be exported in commonly used formats.

(Run a script to generate some thumbnails for publication)


OMERO also offers a web browser-based client which gives access to the key functionality of OMERO through the convenience of the World Wide Web.

(Show web client login and navigation through data manager, open an image in full viewer)


OMERO allows archiving and storage of original images, and routine backup of all data held by the OMERO server can be easily configured.


OMERO and Bioformats are Open Source Projects and support from their thriving community of developers and users ensures there is continual enhancement of existing functionality and development of new features for the software.

(Show forums, trac and some code snippets in IDE, architecture diagram)


OMERO works hand-in-hand with other applications such as imageJ and Matlab for extended manipulation and analysis. OMERO clients can be freely adapted for specific uses. One such use has been adaption of the web client for use in teaching histology

(Show use of imageJ plug-in)


Notes:


Use wide aspect ratio - 16:9
Need to set up a user (?Kyle) with some of Jason's images to use for this.
Make user member of two or three groups.
Identify and note:

• image with z-stack
• image with t-stack
• image with ROI in it

Do screen captures

• use movie capture and static screenshots
• short sequences fine
• no audio needed for movie captures
• after action, remove cursor from capture window (allows easier editing)

Do captions and voice-over subsequently
Aim for 2 minutes - 3 minutes absolute maximum


List of assets needed:


OMERO logo
Bioformats logo
Pictures of microscope
Images from Jason's collection


Movie capture:

• show data manager
• show projects and dataset
• opening image with ROI
• show ROI
• zoom in

Movie capture:

• importing of 3 of images
• show use of file navigator and creation of new Project and use file name for dtataset

Movie capture:

• scrolling down the compatibility table from Bioformats website

Movie capture:

• shot of image viewer
• open metadata panel
• show original metadata

Movie capture:

• data manager
• add groups
• add users
• move data from one group into another
• create new group called "New Paper"
• add 2 users to it

Movie capture:

• open image in viewer
• zoom in
• scroll across image using mouse
• zoom in some more

Movie capture:

• step through Z-stack
• play through Z-stack
• step through t-stack
• play through t-stack

Movie capture:

• renderings panel
• knock out colour channels in turn
• change the intensity of one channel
• show split view

Movie capture:

• draw line ROI
• draw ellipse ROI
• show intensity measurements along line ROI

Movie capture:

• select four thumbnails in middle panel
• run script to generate thumbnails for publication
• open completed output image from attachments

Movie capture:

• show web client login
• navigation through data manager
• open an image in full viewer
• adjust rendering

Still capture:

• forums
• trac
• code in IDE

[rkferguson]

Script V1.0

Welcome to OMERO.
(Logo and montage of microscope and images)


(Warning message: In places sequences have been shortened and some actions omitted)


This movie shows you what you are able to do with your image data and OMERO.
(Quick sequence of data manager, opening image, showing ROI)


OMERO clients run on your computer and connect to a central server run by your institution which stores and manages your image data. OMERO is fully cross-platform, with clients and servers running on Windows, Mac and Linux platforms.
(Downloading Insight client and Unzipping it - different platforms)


OMERO uses the Bioformats engine to import over 120 image data formats including the metadata such as the microscope settings associated with the images. The list of supported formats is constantly updated and expanded.
(Shot scrolling down compatibility table from Bioformats)


You need to import your data into the OMERO server from a local or networked disc.
(Importing of a number of images)
(SL Note: For this section then you can show a further set of files that can be imported linked from Bio-formats point above)


Images and the metadata are stored on the server in the OME-TIFF format which uses an open XML standard to store the metadata along with the pixel data.
(Shot of image viewer with metadata panel showing)
(SL Note: This is key giving scientists access to metadata that they would not previously have, tricky to use words like XML - just need a sense of what it actually means through this point)


You can use OMERO to collaborate with colleagues, creating groups allowing data to be shared between collaborators and co-workers
(Adding groups and users to the data manager, moving data into other groups, create new group and add users to it)


Images can be viewed, zoomed, scrolled through and rendering settings adjusted with the image viewer.
(Open image viewer and zoom, scroll across image)


Z- and t-stacks can be navigated through
(Step through Z-stack and then play through it, play through time stack)


Colour renderings can be adjusted
(Open renderings panel, change from colour to monochrome and back again, knock out colour channels in turn, change the intensity of one channel)


Regions of Interest can be drawn on images and analysis done on these regions. These ROIs can be applied to all images in a dataset
(Draw line ROI and ellipse ROI, show intensity measurements along line, apply ROIs across dataset)
(SL Note: Might be worth showing the rendering settings apply to all option here so one rendering setting is done and then the option to apply to all images in the dataset i.e. 10-15 images maybe - can be very useful for the scientists as a shortcut and timesaving option)


Images can be output and results of analysis exported in commonly used formats. Figures for publication or movies are created by running scripts on selected images
(Run a script to generate some thumbnails for publication)


OMERO also offers a web browser-based client which gives access to the key functionality of OMERO through the convenience of the World Wide Web.
(Show web client login and navigation through data manager, open an image in full viewer)


OMERO allows archiving and storage of original images, and routine backup of all data held by the OMERO server can be easily configured.


OMERO and Bioformats are Open Source Projects and support from their thriving community of developers and users ensures there is continual enhancement of existing and development of new functionality for the software.
(Show forums, trac and some code snippets in IDE, architecture diagram)


OMERO works hand-in-hand with other applications such as imageJ and Matlab for extended manipulation and analysis. OMERO clients can be freely adapted for specific uses. One such use has been adaption of the web client for use in teaching histology
(Show use of imageJ plug-in and some screenshots of Paul Felts' images)
(SL Note: Do you need to check with Paul for this?)


Notes:


Use wide aspect ratio - 16:9
Need to set up a user (?Kyle) with some of Jason's images to use for this.
Make user member of two or three groups.
Identify and note:

• image with z-stack
• image with t-stack
• image with ROI in it

Do screen captures

• use movie capture and static screenshots
• short sequences fine
• no audio needed for movie captures
• after action, remove cursor from capture window (allows easier editing)

Do captions and voice-over subsequently
Aim for 2 minutes - 3 minutes absolute maximum

List of assets needed:

OMERO logo
Bioformats logo
Pictures of microscope
Images from Jason's collection


Movie capture:

• show data manager
• show projects and dataset
• opening image with ROI
• show ROI
• zoom in

Movie capture:

• downloading Insight client
  • Windows
  • Mac
• unzipping and launching
  • Windows
  • Mac

Movie capture:

• importing of 3 of images
• show use of file navigator and creation of new Project and use file name for dtataset

Movie capture:

• scrolling down the compatibility table from Bioformats website

Movie capture:

• shot of image viewer
• open metadata panel
• show original metadata

Movie capture:

• data manager
• add groups
• add users
• move data from one group into another
• create new group called "New Paper"
• add 2 users to it

Movie capture:

• open image in viewer
• zoom in
• scroll across image using mouse
• zoom in some more

Movie capture:

• step through Z-stack
• play through Z-stack
• step through t-stack
• play through t-stack

Movie capture:

• renderings panel
• change from colour to monochrome and back again
• knock out colour channels in turn
• change the intensity of one channel
• show split view

Movie capture:

• draw line ROI
• draw ellipse ROI
• show intensity measurements along line ROI

Movie capture:

• select four thumbnails in middle panel
• run script to generate thumbnails for publication
• open completed output image from attachments

Movie capture:

• show web client login
• navigation through data manager
• open an image in full viewer
• adjust rendering

Diagram showing architecture - from Paul Felts slide
Still capture:

• Paul Felts image (from slides)

NB. get permission from Paul to use


Still capture:

• forums
• trac
• code in IDE

[rkferguson]

Final draft at: squig at: team > Movies > MoviesFor4_4 > OMERO_Showcase_Movie.mov for feedback.

[rkferguson]

Script Final Version

Welcome to OMERO.

(Omero logo - fade out)

OMERO is part of the Open Microscopy Environment, an open-source project which produces tools to support data management for biological light microscopy and also for other imaging applications.
(OME Logo with Open Microscopy Environment above and www.openmicroscopy.org underneath - change to add in OMERO and Bioformats logos above)

(Montage of microscopy/plate images)

The OMERO clients run on your computer and connect to a central server run by your institution which stores and manages your image data.

(Screenshots of clients with platform logos)

(Database graphic with platform logos)

The system is fully cross-platform, with both clients and servers running on Windows, Mac and Linux platforms.

(Screenshots of OMERO data manager on three platforms)

Using OMERO you can import image data from local and networked drives and store them in a central server. The original metadata is read by Bioformats and imported with the image into the OMERO database.

(Speeded up import movie)

Metadata such as the name of the microscope and any settings is preserved and any further data added or changes made to the image rendering settings in OMERO can be saved and are stored separately.

(Shows imported data in the data manage, thumbnails the acquisition and renderings tabs in the right hand pane.)

The Bioformats engine is used by OMERO to import image data with over 120 image data formats currently supported. The list of supported formats is constantly being updated and expanded.

(Bioformats still image)

The OMERO system allows you to create groups of users with different levels of permissions for viewing and working with data. This allows you to collaborate with colleagues on shared image data at different levels according to how the permissions are set.

(Show groups in data manager)

The image viewer allows you zoom into images, scroll across them and adjust rendering settings and the colours assigned to the different channels.

(Double click on image in data tree to open viewer and illustrate above points)

Where present, Z- and t-stacks can be navigated by stepping or playing through them.
(Step through and play through z stack)

Measurement and analysis of image data can be performed.

(Use image that has ROI on it - have analysis pane open at histogram - resized to match image viewer)

Graphs of intensities can be displayed or tables of results viewed and downloaded. The ROIs are easily applied to all images in a dataset, and can be labelled and saved to the database.

(Click to table and export as Excel spreadsheet. Click to cancel and click checkbox show text with ROI)

OMERO works hand-in-hand with many other applications such as imageJ and Matlab for extended manipulation and analysis of image data.

(Show opening of OMERO plugin in ImageJ)

The results from any analysis can be exported in commonly used formats for publication or further analysis, and a number of other export options are available using scripts, including the output of image data as figures or as movies.

(Show scripts available and create thumbnails figure)

There is also a web browser-based client which gives you access to the key functionality of OMERO through the convenience of the World Wide Web.

(Show web client, opening image using link to open in new browser window, zoom and scroll.)

OMERO and Bioformats are Open Source Projects and support from their thriving community of developers and users ensures there is continual enhancement of existing functionality and development of new features for the software.

(OME with OMERO and Bioformats logos. Show screenshot of forums page and QA)

Under the G-N-U General Public License the OMERO system can be freely adapted for specific uses by groups or institutions.

(Closing image with OME logo centre and OMERO and Bioformats logos with GNU and commercial licensing information)

(Data attribution)

Thank you for watching this presentation.

(OME logo centre - video produced under CCL)