SWC-Advanced-Microscopy BakingTray issues

SWC-Advanced-Microscopy / BakingTray

Serial-section automated anatomy extension for ScanImage

https://bakingtray.mouse.vision/

GNU Lesser General Public License v3.0

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issues

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Where are the on-screen stage limits?

#466 raacampbell opened 2 weeks ago
0
The stop button popup is not pausing the acquisition

#465 raacampbell opened 2 weeks ago
0
If vDAQ the external trigger is on D0.0 for tile scans. This can't be used for anything else like reso sync

#464 raacampbell opened 2 weeks ago
0
Doing "New Sample" before lowering the stage causes only 1 section to be imaged

#463 raacampbell opened 2 months ago
0
NV repeatedly reports laser on after it's been turned off

#462 raacampbell opened 2 months ago
0
Make Stop dialog clearer: people keep initiating stitching

#461 raacampbell opened 2 months ago
0
Resume failed because ScanImage though it was still in acquisition mode, even though it appeared to be stopped

#460 raacampbell opened 2 months ago
0
Wrong channel displayed in Preview Window after autothresh

#459 raacampbell opened 3 months ago
0
error message cryptic if adding a laser calibration without BakingTray started

#458 raacampbell closed 4 months ago
1
where should doResetPMTs live? SIBT or main config?

#457 raacampbell closed 4 months ago
1
Sample VP_CAP65 just stopped with the laser seemingly trying to turn off half way through

#456 raacampbell opened 4 months ago
0
Document changes to the YML for the raise button

#455 raacampbell closed 4 months ago
0
Update "Frames" when user alters "Averaging"

#454 raacampbell closed 4 months ago
1
Slimming down some of the move checks might save us up to 100 ms per motion

#453 raacampbell opened 8 months ago
0
Check that raw data tiffs all have the same size.

#452 raacampbell opened 10 months ago
0
Laser comms fails and acquisition stops randomly (rare)

#451 raacampbell opened 11 months ago
0
Overlap proportion is not correct

#450 raacampbell opened 1 year ago
0
Saved recipe sometimes has voxelSize saved incorrectly

#449 raacampbell closed 4 months ago
2
Preview scan randomly does not start. Seems related to ROI drawing

#448 raacampbell opened 1 year ago
1
Add option to resume *this* acquisition (or similar)

#447 raacampbell opened 1 year ago
0
Averaging was set to 2 in section 2 and on resume is 1

#446 raacampbell opened 1 year ago
0
Warning message on recipe mismatch during resume does not say which the setting is

#445 raacampbell opened 1 year ago
0
FOV square does not appear until user moves stage

#444 raacampbell closed 1 year ago
1
autoROI acquisition failed to expand tissue after a certain point

#443 raacampbell opened 1 year ago
1
Since last merge into master, the laser power values are missing from the GUI

#442 raacampbell closed 4 months ago
1
Hold hand of user after resume

#441 raacampbell opened 1 year ago
0
Document what lock z does

#440 raacampbell closed 1 year ago
1
Cutting start point does not update in prepare GUI after restart of acquisition

#439 raacampbell opened 1 year ago
1
Start tmux session for S&C from BakingTray menu

#438 raacampbell opened 1 year ago
1
Bake ended with a bounding box error and never made FINISHED file

#437 raacampbell opened 1 year ago
1
There is no check that the PIFOC has sufficient range to image the requested range of depths

#436 raacampbell opened 2 years ago
1
Record where possible power in mW at the sample

#435 raacampbell opened 2 years ago
1
Update mW at sample displayed by ScanImage when laser changes wavelength

#434 raacampbell opened 2 years ago
4
Set fast preview scan parameters for galvos in the system settings YAML

#433 raacampbell opened 2 years ago
0
Using multiple channels in BakingTray creates a problem in SI 2021

#432 raacampbell closed 2 years ago
1
PMT trip reset fails in SI 2021

#431 raacampbell closed 2 years ago
1
manually setting the x cut value does not set the Y cut value

#430 raacampbell closed 2 years ago
1
Add a "load" button

#429 raacampbell closed 4 months ago
2
Pockels switches off on BakingTray startup

#428 raacampbell opened 2 years ago
1
Look into finding hSI with findobj instead of going via evalin

#427 raacampbell opened 2 years ago
1
Preview scans have a harmless error message with ScanImage(R) Basic 2021.1.0 2af5d7cfec

#426 raacampbell closed 2 years ago
1
Directory name selected by the user is not screened for weird characters.

#425 raacampbell closed 4 months ago
2
Sample rename in same directory somehow got through the acquisition start checks

#424 raacampbell opened 2 years ago
2
Acquisitions that fail when brain is small may not be sending a Slack message

#423 raacampbell closed 2 years ago
0
Objective depth should be re-applied on resume

#422 raacampbell opened 2 years ago
1
Resume acquisition needs to cd to sample directory for the file move step to work

#421 raacampbell closed 1 year ago
2
Prerelease

#420 DGunton closed 2 years ago
1
If user closes SI channel windows the channels to display is empty and that stops s&crunch until first section is complete

#419 raacampbell closed 2 years ago
1
Front/left corner of slide is likely a bad convention if someone mounts the vibratome on the left

#418 raacampbell opened 2 years ago
0
Document on WWW blade/slide pos

#417 raacampbell closed 4 months ago
0