Opened 7 years ago

Closed 7 years ago

#371 closed task (fixed)

Wizard that move histology samples to paraffin blocks

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: Reggie v2.7
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

We need a couple of histology processing wizards. The current samples are stored in temporary bioplates (HisNNNN). The bioplates are currently a "generic storage" type, but this should manually be changed to a "Histology" box type (9x9 geometry).

This wizard should allow the operator to select an existing histology box existing Histology items and move the biomaterial to new 3x2 "Paraffin block" bioplates. The list with existing Histology items should only include those without a creation date and it should be sorted by bioplate and position. The biomaterial is automatically moved row-by-row to the paraffin blocks in the order: C1, B1, A1, C2, B2. The A2 position is left empty. The wizard should create full paraffin blocks only. Remaining items should be left in the original box. The wizard should also set the creation date, protocol, and other properties related to the embedding.

Paraffin blocks should be autonamed using a prefix and running number: PB000001, etc.

Change History (12)

comment:1 Changed 7 years ago by Nicklas Nordborg

Milestone: Reggie v2.5
Status: newassigned

comment:2 Changed 7 years ago by Nicklas Nordborg

(In [1589]) References #371: Wizard that move histology samples to paraffin blocks

First version of the wizard. It should do most of what is needed already.

Installation wizard is creating/checking a few more items that are needed.

Added text file with test data.

The wizard need to store creation date on bioplates which means that BASE 3.1 is needed.

comment:3 Changed 7 years ago by Nicklas Nordborg

Milestone: Reggie v2.5Reggie v2.7

comment:4 Changed 7 years ago by Nicklas Nordborg

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

comment:5 Changed 7 years ago by Nicklas Nordborg

(In [1621]) References #371: Wizard that move histology samples to paraffin blocks

Do not install items that are used by the histology wizards since it has been postponed to Reggie 2.7

comment:6 Changed 7 years ago by Nicklas Nordborg

(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:7 Changed 7 years ago by Nicklas Nordborg

Description: modified (diff)

comment:8 Changed 7 years ago by Nicklas Nordborg

(In [1683]) References #371: Wizard that move histology samples to paraffin blocks

This wizard has been changed to start with a 'Histology working list' instead of a bioplate.

comment:9 Changed 7 years ago by Nicklas Nordborg

(In [1684]) References #371 and #372. Create (empty) paraffin block plates at the same time as the work lists are created otherwise the plate names on the lab tracking protocol may not match plate names that would have been generated by the registration wizard.

The registration wizard can now select a protocol (Histology subtype).

comment:10 Changed 7 years ago by Nicklas Nordborg

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

comment:11 Changed 7 years ago by Nicklas Nordborg

(In [1692]) References #371: Wizard that move histology samples to paraffin blocks

Added step for recording storage box for the blocks.

comment:12 Changed 7 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

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

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