Notice: In order to edit this ticket you need to be either: a Product Owner, The owner or the reporter of the ticket, or, in case of a Task not yet assigned, a team_member"

Task #11318 (new)

Opened 6 years ago

Last modified 4 years ago

EMBL-Heidelberg Format

Reported by: ajpatterson Owned by:
Priority: minor Milestone: Unscheduled
Component: Bio-Formats Version: 4.4.8
Keywords: new-format Cc:
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

Review the files for the mDigital Scanning Lightsheet / EMBL-Heidelberg Format sumbitted to QA: 7540.

Related details on forum: https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=5804


Just started working with a SPIM scope that writes each stack in a separate tiff file. Was wondering if it would be possible to have bioformats recognise the format and read all the stacks as one big movie.

Have uploaded a dataset for you guys with ID 7540.

The microscope is a mDigital Scanning Lightsheet microscope. Its an in-house built by EMBL-Heidelberg and to be honest I don't think they have a website.
I will try and find out the version of the software that created the files.

I realize that this is a very much niche file format so would understand if you guys can't really do much about it.

Change History (2)

comment:1 Changed 5 years ago by mlinkert

  • Keywords new-format added

comment:2 Changed 4 years ago by mlinkert

  • Owner mlinkert deleted

This should be pretty straightforward - pixel data is stored in plain TIFFs (which we already read), with metadata in a separate easily readable XML file. I'd expect the QA above to contain two datasets, with the .xlsfm from each being the target for setId. This would be a good first reader.

Note: See TracTickets for help on using tickets. You may also have a look at Agilo extensions to the ticket.

1.3.13-PRO © 2008-2011 Agilo Software all rights reserved (this page was served in: 0.97993 sec.)

We're Hiring!