Opened 7 years ago

Closed 6 years ago

#373 closed task (fixed)

Register HE glass and histology child items

Reported by: nicklas Owned by: nicklas
Priority: major Milestone: Reggie v2.7
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

The paraffin blocks from #371 are sectioned and placed on glass slides. The layout on the glass is mirrored from the paraffin blocks (A1->A2, B1->B2, B2->B1, C1->C2, C2->C1) The A1 position is empty on the glass slides.

Depending on the quality, each paraffin block may have multiple sections. The lab protocol from #372 is used to record the best slide for each sample.

The wizard should allow the user to select a single paraffin block at a time. The default list should include unprocessed paraffin blocks but it should be possible to manually select any block. The next step show the 5 samples and the user should enter the index number of the best HE stained sample. Reggie should create as many child HE glass plates as is needed and create child biomaterial in each of the five used positions with suffix .he1, .he2, etc. The best samples should be annotated with a boolean "GoodStain?" annotation.

Change History (12)

comment:1 Changed 7 years ago by nicklas

  • Milestone set to Reggie v2.5

comment:2 Changed 6 years ago by nicklas

  • Milestone changed from Reggie v2.5 to Reggie v2.7

comment:3 Changed 6 years ago by nicklas

(In [1612]) References #371, #372, #373. Remove links to Histology wizards since we will wait with this until Reggie 2.7.

comment:4 Changed 6 years ago by nicklas

  • Status changed from new to assigned

comment:5 Changed 6 years ago by nicklas

(In [1666]) References #371, #372, #373. Fix things that was removed/disabled in [1612] and [1621] due to the delay of the Histology wizards.

comment:6 Changed 6 years ago by nicklas

(In [1668]) References #373: Register HE glass and histology child items

The wizard can now crete child HE plates and biomaterial items on them. The "GoodStain?" annotation is used to mark one of the child biomaterial items. The wizard can also be used to update existing child plates.

comment:7 Changed 6 years ago by nicklas

(In [1685]) References #371, #372 and #373. Synchonized names with existing items on the production server.

comment:8 Changed 6 years ago by nicklas

(In [1686]) References #373: Register HE glass and histology child items

Added protocol to the form.

comment:9 Changed 6 years ago by nicklas

(In [1687]) References #373: Register HE glass and histology child items

Fixes incorrect filter due to the name change in [1685]. Make the filter temporary.

comment:10 Changed 6 years ago by nicklas

(In [1694]) References #373: Register HE glass and histology child items

Added step for recording storage box and position for the glass slides. The registration should work, but there is no validation or "smart" functions for auto-generating values yet.

comment:11 Changed 6 years ago by nicklas

(In [1695]) References #373: Register HE glass and histology child items

Added code that finds the last used storage box and position for HE glass and then use that to automatically suggest locations for new slides.

comment:12 Changed 6 years ago by nicklas

  • Resolution set to fixed
  • Status changed from assigned to closed

Closing this so that 2.7 can be released. If changes/fixes are needed, new tickets should be created.

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