Opened 13 years ago

Closed 12 years ago

#373 closed task (fixed)

Register HE glass and histology child items

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
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 by Nicklas Nordborg, 13 years ago

Milestone: Reggie v2.5

comment:2 by Nicklas Nordborg, 13 years ago

Milestone: Reggie v2.5Reggie v2.7

comment:3 by Nicklas Nordborg, 13 years ago

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

comment:4 by Nicklas Nordborg, 13 years ago

Status: newassigned

comment:5 by Nicklas Nordborg, 13 years ago

(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 by Nicklas Nordborg, 13 years ago

(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 by Nicklas Nordborg, 13 years ago

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

comment:8 by Nicklas Nordborg, 13 years ago

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

Added protocol to the form.

comment:9 by Nicklas Nordborg, 13 years ago

(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 by Nicklas Nordborg, 13 years ago

(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 by Nicklas Nordborg, 13 years ago

(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 by Nicklas Nordborg, 12 years ago

Resolution: fixed
Status: assignedclosed

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

Note: See TracTickets for help on using tickets.