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Add Tecan Spark Cyto reader #3637

Merged
merged 14 commits into from
Dec 14, 2020
Merged

Add Tecan Spark Cyto reader #3637

merged 14 commits into from
Dec 14, 2020

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melissalinkert
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Backported from a private PR. The new reader adds support for data from this acquisition system: https://lifesciences.tecan.com/plate-reader-live-cell-imaging-cytometry

Plates consist of a sqlite database file, a directory hierarchy containing TIFFs, and optional analysis results in various formats. Only the sqlite database can be accepted by setId. No test data yet, but opening the PR now to verify that no existing tests are affected.

As this is a new reader with a new dependency, a minor release will be necessary.

@sbesson
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sbesson commented Nov 20, 2020

Excluding as this failed the nightly repository build. In particular this affects filesets containing Thumbs.db e.g.

   [testng] The factory method class loci.tests.testng.FormatReaderTestFactory.createInstances() threw an exception
   [testng] [2020-11-20 00:43:49,859] [main] setId("/data/karen/Thumbs.db") failed
   [testng] java.io.IOException: Cannot find expected 'Images' directory
   [testng] 	at loci.formats.in.TecanReader.initFile(TecanReader.java:234) ~[formats-gpl-6.6.0-SNAPSHOT.jar:6.6.0-SNAPSHOT]
   [testng] 	at loci.formats.FormatReader.setId(FormatReader.java:1421) ~[formats-api-6.6.0-SNAPSHOT.jar:6.6.0-SNAPSHOT]
   [testng] 	at loci.formats.ImageReader.setId(ImageReader.java:849) ~[formats-api-6.6.0-SNAPSHOT.jar:6.6.0-SNAPSHOT]
...

@melissalinkert
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a730fe7 should fix the build failures, but I'll re-exclude if the next build that includes this PR is still failing.

@melissalinkert
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Two test plates are now in inbox/tecan/, see configuration in https://github.com/openmicroscopy/data_repo_config/pull/480

@sbesson
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sbesson commented Dec 8, 2020

Imported the sample plates into a server with this reader included without any issue

Screenshot 2020-12-07 at 15 49 28
Screenshot 2020-12-07 at 16 36 26

All the metadata populated by the reader is present (pixel sizes, channel names, acquisition date, exposure times). And the binary data reads as expected. Only puzzlement from my side is why the image names are named after the DB filename rather than the plate name. I think this is related to the behavior discussed ome/design#57 but we had updated the code to trust the Plate.Name metadata set by reader.

I'll leave David to take a look at the source code.

melissalinkert added a commit to melissalinkert/bio-formats-documentation that referenced this pull request Dec 9, 2020
@dgault dgault added this to the 6.6.0 milestone Dec 14, 2020
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dgault commented Dec 14, 2020

Source code for the new reader looks good and manual testing of the 2 sample plates also shows no issues and both pixel and metadata look to be read and displayed correctly. All unit tests and repo tests continue to pass with this new reader and the associated config included. Merging for inclusion in 6.6.0

@dgault dgault merged commit 75958d7 into ome:develop Dec 14, 2020
@melissalinkert melissalinkert deleted the tecan-develop branch May 20, 2021 22:27
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3 participants