Opened 6 years ago

Closed 6 years ago

#489 closed task (fixed)

Histology scoring wizard

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v2.14
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

This is a new wizard in the Histology section. It should be used to add scores to the H&E stained samples on glass slides.

The wizard should work with one glass at a time, in the order they have been stored in the storage box (eg. sort by tray and position). For each glass slide it should be possible to enter several scores which are percentage counts of various cell types found in the sample. There are currently 6 groups (need to check what they are called). The wizard should check that they sum up to 100%.

The default "mode" is that scores should be entered for each sample that has the GoodStain annotation. Note that some slides may have no such sample so it must be possible to register that slide as done so that it doesn't reappear the next time the wizard is started.

It should be possible to score samples not having the GoodStain annotation as well and then there should be an optional possibility to take over the GoodStain annotation from the sister sample on another slide.

It should also be possible to register incomplete results. The slide should then be marked as such so that it is possible to quickly find it and complete the information at a later time.

It should also be possible to redo any completed slide.

Change History (12)

comment:1 Changed 6 years ago by Nicklas Nordborg

(In [2117]) References #489: Histology scoring wizard

  • Added 7 new annotations for keeping the scores.
  • Added entry point for the scoring wizard on the Reggie start page.
  • Implemented counting of unscored HE glass
  • Started with method for loading the information that is needed to be able to score a set of HE glass.

comment:2 Changed 6 years ago by Nicklas Nordborg

Status: newassigned

comment:3 Changed 6 years ago by Nicklas Nordborg

(In [2123]) References #489: Histology scoring wizard

Information about the next set of HE glass is now retreived and a GUI is created. There is functionality for selecting which sample to score, enter scores and setting the GoodStain annotation. Some validation has been implemented, but it is not possible to save data back to BASE. Manually selecting a different HE glass is not implemented.

comment:4 Changed 6 years ago by Nicklas Nordborg

Milestone: Reggie v2.xReggie v2.14

comment:5 Changed 6 years ago by Nicklas Nordborg

(In [2124]) References #489: Histology scoring wizard

Implemented 'Find HE glass', 'Select HE glass' and menu with uncompleted HE glass functions.

comment:6 Changed 6 years ago by Nicklas Nordborg

(In [2125]) References #489: Histology scoring wizard

Implemented saving of scores. There are still some rough corners and error handling to take care of.

comment:7 Changed 6 years ago by Nicklas Nordborg

(In [2128]) References #489: Histology scoring wizard

Several improvements to saving and error handling:

  • Support for 'keep session alive' to reduce the risk of automatic logout during data entry
  • Warning about unsaved data should now work for all cases when navigating to another page
  • Using local storage to temporary store info on the local computer. Useful if computer/browser crashes and it is possible to restore all entered information.

comment:8 Changed 6 years ago by Nicklas Nordborg

(In [2129]) References #489: Histology scoring wizard

Do not ask about 'unsaved modifications' when there are no modifications.

comment:9 Changed 6 years ago by Nicklas Nordborg

(In [2130]) References #489: Histology scoring wizard

Adding links from HE and PB bioplates (list view and single item view) to the scoring wizard.

comment:10 Changed 6 years ago by Nicklas Nordborg

(In [2131]) References #489: Histology scoring wizard

Added score information to case summary page.

comment:11 Changed 6 years ago by Nicklas Nordborg

(In [2134]) References #489: Histology scoring wizard

Merge development branch (brances/ticket-489) to trunk.

comment:12 Changed 6 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed
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