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Task #13085 (closed)

Opened 4 years ago

Closed 4 years ago

BUG: Leica Lif reader (Mapping lasers to channels issue)

Reported by: bramalingam Owned by: mlinkert
Priority: minor Milestone: B-F-5.1.6
Component: Bio-Formats Version: 5.0.5
Keywords: n.a. Cc: lingfengtang1982@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

ref: http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-October/005700.html

Testing results:
Issue was reproducible, the ome-xml seems to pick up all the lasers. But the mapping of the lasers to the channels seems to be off.

Attachments (2)

Screenshot (2).png (221.4 KB) - added by mlinkert 4 years ago.
Screenshot (3).png (226.6 KB) - added by mlinkert 4 years ago.

Download all attachments as: .zip

Change History (3)

comment:1 Changed 4 years ago by mlinkert

  • Resolution set to invalid
  • Status changed from new to closed

Closing as invalid - upon closer inspection, I do think we are doing the correct thing here.

Leica's LAS X software shows more detailed information about the lasers (screenshots are attached). It shows 4 lasers (405 Diode, Argon, DPSS 561, HeNe? 633), the latter 2 of which are "On", and the former 2 of which are "Off" or "0%". In the "Sequential Setting" sections (per-channel instrument configuration), only the 561nm laser line is active for section 1, and only the 633nm laser line is active for section 2. There is nothing in the software or the file's XML metadata to indicate that the 488nm laser was ever activated during the acquisition. The "633" in the file name does suggest that the 633nm laser was used as well (as spotted by Balaji).

If it's absolutely certain that the 488nm laser was used, and the 633nm laser was not, then we'll need some assistance in locating which metadata from Leica's software actually shows that this is the case.

Changed 4 years ago by mlinkert

Changed 4 years ago by mlinkert

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