Acquisition Metadata

[jburel]

Meeting 02/0908

Goal: store as much acquisition data as possible.

Some information are coming from the file itself (usually the settings) and other information like microscope, objective etc have to be entered manually.

Anticipated workflow

• Person in charge of the microscopy facility, will enter the Instrument details (see OME Data model)
• User will create his/her Image Acquisition Profile and his/her Channel Acquisition Profile save the profile back to the OMERO server.
• Before/During/After import, the user will link the created profile to the image, the acquisition settings retrieved from the image file will be linked to the image

The Image Acquisition Profile and Channel Acquisition Profile will be described as Structured Annotations in the Data Model but should have specific entries in the DB.

Profiles' Description

Image Acquisition Profile

• name: String
• description: String
• microscopeID: long
• objectivedID: long (one of the objectives attached to the selected microscope)

Channel Acquisition Profile

• name: String
• description: String
• detectorID: long
• filterSetID: long
• lightSourceID: long
• OTFID: long

TODO: Check multiple lightsources case.

Note: A profile belongs to a given user

Manual metadata input

Questions:

• Workflow: Start with "Add Instrument" or start with "Add Filter"?
• Flexibility: Don't want fields to be "required" if data is not commonly available.
• Generic Names: Do I need to name a filter "DAPI - excitation" or name a filter-set "DAPI"?
• Do users need to create their own filter-sets, or simply pick from pre-defined filter-sets?

Actions

• Melissa: Parse file provided to extend metadata support. Starting with DV.
  
• Andrew: model profile with annotation.
  
• J-M, Will: start thinking of implementation of UI workflow
• Brian: Adjust import when metadata available

[jburel]

Replying to jburel:

== Meeting 02/0908 == Goal: store as much acquisition data as possible.
Some information are coming from the file itself (usually the settings) and other information like microscope, objective etc have to be entered manually. == Anticipated workflow == * Person in charge of the microscopy facility, will enter the Instrument details (see OME Data model) * User will create his/her Image Acquisition Profile and his/her Channel Acquisition Profile save the profile back to the OMERO server. * Before/During/After import, the user will link the created profile to the image, the acquisition settings retrieved from the image file will be linked to the image The Image Acquisition Profile and Channel Acquisition Profile will be described as Structured Annotations in the Data Model but should have specific entries in the DB. == Profiles' Description == Image Acquisition Profile
* name: String * description: String * microscopeID: long * objectivedID: long (one of the objectives attached to the selected microspoque) Channel Acquisition Profile
* name: String * description: String * detectorID: long * filterSetID: long * lightSourceID: long * OTFID: long TODO: Check multiple light source case.
Note: A profile belongs to a given user == Actions == * Melissa: Parse file provided to extend metadata support. Starting with DV.
* Andrew: model profile with annotation.
* J-M, Will: start thinking of implementation of UI workflow * Brian: Adjust import when metadata available

[jburel]

How to collect microscope/detector etc data

• Will has used Django to expose the model in a "user friendly way". Meeting with Sam planned.
• JM: when I have a bit of time, will play with Java UI. Will and I discussed few things around a cup of coffee: apparently coffee helps to think.