SWC-Advanced-Microscopy/BakingTray

Issues

• Doing "New Sample" before lowering the stage causes only 1 section to be imaged

  #463 opened 7 months ago by raacampbell
  0

• NV repeatedly reports laser on after it's been turned off

  #462 opened 7 months ago by raacampbell
  0

• Make Stop dialog clearer: people keep initiating stitching

  #461 opened 7 months ago by raacampbell
  0

• Resume failed because ScanImage though it was still in acquisition mode, even though it appeared to be stopped

  #460 opened 7 months ago by raacampbell
  0

• Wrong channel displayed in Preview Window after autothresh

  #459 opened 8 months ago by raacampbell
  0

• Document on WWW blade/slide pos

  #417 opened 9 months ago by raacampbell
  0

• Document changes to the YML for the raise button

  #455 opened 9 months ago by raacampbell
  0

• error message cryptic if adding a laser calibration without BakingTray started

  #458 opened 9 months ago by raacampbell
  1

• where should doResetPMTs live? SIBT or main config?

  #457 opened 9 months ago by raacampbell
  1

• Document on WWW Pockels power gating

  #416 opened 9 months ago by raacampbell
  0

• Document on WWW RPM for motor

  #415 opened 9 months ago by raacampbell
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• Sample VP_CAP65 just stopped with the laser seemingly trying to turn off half way through

  #456 opened 9 months ago by raacampbell
  0

• There is no check that the PIFOC has sufficient range to image the requested range of depths

  #436 opened 2 years ago by raacampbell
  1

• Saved recipe sometimes has voxelSize saved incorrectly

  #449 opened 9 months ago by raacampbell
  2

• Update "Frames" when user alters "Averaging"

  #454 opened 9 months ago by raacampbell
  1

• Update mW at sample displayed by ScanImage when laser changes wavelength

  #434 opened 3 years ago by raacampbell
  4

• Add a "load" button

  #429 opened 9 months ago by raacampbell
  2

• Since last merge into master, the laser power values are missing from the GUI

  #442 opened 9 months ago by raacampbell
  1

• Record where possible power in mW at the sample

  #435 opened 2 years ago by raacampbell
  1

• Directory name selected by the user is not screened for weird characters.

  #425 opened 10 months ago by raacampbell
  2

• Slimming down some of the move checks might save us up to 100 ms per motion

  #453 opened a year ago by raacampbell
  0

• Check that raw data tiffs all have the same size.

  #452 opened a year ago by raacampbell
  0

• Laser comms fails and acquisition stops randomly (rare)

  #451 opened a year ago by raacampbell
  0

• Overlap proportion is not correct

  #450 opened 2 years ago by raacampbell
  0

• Preview scan randomly does not start. Seems related to ROI drawing

  #448 opened 2 years ago by raacampbell
  1

• Resume acquisition needs to cd to sample directory for the file move step to work

  #421 opened 2 years ago by raacampbell
  2

• FOV square does not appear until user moves stage

  #444 opened 2 years ago by raacampbell
  1

• Add option to resume *this* acquisition (or similar)

  #447 opened 2 years ago by raacampbell
  0

• Averaging was set to 2 in section 2 and on resume is 1

  #446 opened 2 years ago by raacampbell
  0

• Warning message on recipe mismatch during resume does not say which the setting is

  #445 opened 2 years ago by raacampbell
  0

• autoROI acquisition failed to expand tissue after a certain point

  #443 opened 2 years ago by raacampbell
  1

• Cutting start point does not update in prepare GUI after restart of acquisition

  #439 opened 2 years ago by raacampbell
  1

• Document what lock z does

  #440 opened 2 years ago by raacampbell
  1

• Hold hand of user after resume

  #441 opened 2 years ago by raacampbell
  0

• Start tmux session for S&C from BakingTray menu

  #438 opened 2 years ago by raacampbell
  1

• Bake ended with a bounding box error and never made FINISHED file

  #437 opened 2 years ago by raacampbell
  1

• PMT trip reset fails in SI 2021

  #431 opened 2 years ago by raacampbell
  1

• Using multiple channels in BakingTray creates a problem in SI 2021

  #432 opened 2 years ago by raacampbell
  1

• Pockels switches off on BakingTray startup

  #428 opened 3 years ago by raacampbell
  1

• Preview scans have a harmless error message with ScanImage(R) Basic 2021.1.0 2af5d7cfec

  #426 opened 3 years ago by raacampbell
  1

• Set fast preview scan parameters for galvos in the system settings YAML

  #433 opened 3 years ago by raacampbell
  0

• manually setting the x cut value does not set the Y cut value

  #430 opened 3 years ago by raacampbell
  1

• Look into finding hSI with findobj instead of going via evalin

  #427 opened 3 years ago by raacampbell
  1

• Objective depth should be re-applied on resume

  #422 opened 3 years ago by raacampbell
  1

• Sample rename in same directory somehow got through the acquisition start checks

  #424 opened 3 years ago by raacampbell
  2

• Acquisitions that fail when brain is small may not be sending a Slack message

  #423 opened 3 years ago by raacampbell
  0

• The recipe of a resumed sample is not updated if parameters are modified

  #413 opened 3 years ago by raacampbell
  2

• If user closes SI channel windows the channels to display is empty and that stops s&crunch until first section is complete

  #419 opened 3 years ago by raacampbell
  1

• The read system settings file lacks some new settings

  #414 opened 3 years ago by raacampbell
  1

• Front/left corner of slide is likely a bad convention if someone mounts the vibratome on the left

  #418 opened 3 years ago by raacampbell
  0