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czbiohub-sf
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shrimPy
shrimPy: Smart High-throughput Robust Imaging & Measurement in Python
BSD 3-Clause "New" or "Revised" License
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Unify CLI call signatures
#65
ieivanov
closed
1 year ago
4
Revert back to checking if acq is finished based on image_saved_fn callback
#64
ieivanov
closed
1 year ago
0
Develop image-based autofocus for LF arm
#63
ieivanov
opened
1 year ago
0
Default number of workers for multiprocessing
#62
ieivanov
closed
3 months ago
6
Mantis uses root logger which captures events from external modules
#61
ieivanov
closed
1 year ago
0
Mantis acq fails silently if wrong config group / config name is provided
#60
ieivanov
opened
1 year ago
0
Average `n=3` slices immediately following deskew
#59
talonchandler
closed
1 year ago
0
Merge slurm deskew with `mantis deskew` CLI call
#57
ieivanov
opened
1 year ago
1
Add documentation on mantis CLI options
#56
ieivanov
closed
1 year ago
1
Registration pipeline
#55
edyoshikun
closed
1 year ago
10
mantis acquisitions save incorrect `z-step_um` metadata
#58
talonchandler
closed
1 year ago
2
Revert "Mantis deskewing with multiprocessing and slurm"
#54
ieivanov
closed
1 year ago
0
Add conda environment logger
#53
ieivanov
closed
1 year ago
0
`estimate-bleaching` from zarr
#52
talonchandler
closed
1 year ago
0
Prime BSI Express camera has high column noise
#51
ieivanov
closed
1 year ago
1
Phase 3D reconstruction and slumkit example
#50
edyoshikun
closed
1 year ago
2
Add microscope setup guide
#49
ieivanov
closed
1 year ago
0
Implement O3 autofocus on light-sheet arm
#48
edyoshikun
closed
1 year ago
1
Mantis deskewing with multiprocessing and slurm
#47
edyoshikun
closed
1 year ago
12
create-then-fill
#46
edyoshikun
closed
1 year ago
6
Control Vortran lasers through `copylot`
#45
edyoshikun
closed
1 year ago
2
Demo scripts to use iohub with SLURM job arrays
#44
ziw-liu
closed
1 year ago
7
IPC diagram
#43
ziw-liu
opened
1 year ago
1
Convert to zarr as an initial analysis step
#42
talonchandler
closed
1 year ago
5
Acquisition finishes but fails to cleanup
#41
edyoshikun
closed
1 year ago
4
Add more testing for missing variables for Channel Settings.
#40
edyoshikun
closed
1 year ago
9
Upgrade PM and MM
#39
talonchandler
closed
1 year ago
9
Triggerscope not resetting after a failed acquisition
#38
edyoshikun
closed
1 year ago
3
Estimate bleaching/experimental lifetimes
#37
talonchandler
closed
1 year ago
0
Update mantis_usage.md fixing typo
#36
edyoshikun
closed
1 year ago
0
Change to a grouped CLI
#35
talonchandler
closed
1 year ago
1
implement nested CLI
#34
ieivanov
closed
1 year ago
0
prototype parallel deskew implementation
#33
ieivanov
closed
1 year ago
3
write positions.csv log during acquisition
#32
ieivanov
closed
1 year ago
1
improve autofocus re-engagement when moving to a new well
#31
ieivanov
closed
1 year ago
2
MVP of napari viewer
#30
ieivanov
opened
1 year ago
3
update data structure docs
#29
ieivanov
closed
1 year ago
0
Documentation on mantis acquisition protocol
#28
edyoshikun
closed
1 year ago
2
multiprocessing model for mantis
#27
mattersoflight
opened
1 year ago
2
Oryx camera may be dropping frames or missing trigger pulses
#26
ieivanov
opened
1 year ago
3
determine correct LS data sampling
#25
ieivanov
closed
1 year ago
2
realign LS remote refocus arm
#24
ieivanov
closed
3 months ago
0
realign LF remote refocus arm
#23
ieivanov
closed
1 year ago
1
Bugfix/acq slowdown
#22
ieivanov
closed
1 year ago
2
Bugfix/autofocus
#21
ieivanov
closed
1 year ago
1
extend the axial imaging depth of the mantis microscope by moving the sample in z
#20
ieivanov
opened
1 year ago
0
Develop image-based autofocus for LS arm
#19
ieivanov
closed
1 year ago
3
add plate hight interpolation
#18
ieivanov
opened
1 year ago
0
add FOV selection based on cell distribution
#17
ieivanov
opened
1 year ago
0
add FOV selection for transmission light imaging
#16
ieivanov
opened
1 year ago
0
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