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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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Better cropping of registered datasets
#115
ieivanov
closed
10 months ago
0
Registration `source` and `target` images should be renamed to `moving` and `fixed`
#114
ieivanov
closed
10 months ago
1
`update-scale-metadata` CLI call needs a docstring
#113
ieivanov
closed
2 months ago
1
Merging the PRs
#112
edyoshikun
closed
3 months ago
1
Slurmkit scripts slowing down the I/O
#111
edyoshikun
opened
12 months ago
0
Mantis processing pipeline
#110
edyoshikun
opened
12 months ago
1
Denoise and illumination background correction
#109
edyoshikun
closed
4 months ago
0
XY and Z drift stabilization
#108
edyoshikun
closed
10 months ago
1
function to merge multiple stores
#107
edyoshikun
closed
5 months ago
1
Segmentation (no CLI)
#106
edyoshikun
closed
4 months ago
1
Only move stage when going to different position
#105
ieivanov
closed
1 year ago
0
More robust acquisition abort
#104
ieivanov
closed
1 year ago
0
Z-drift and XY stabilization
#103
edyoshikun
closed
12 months ago
3
Registration V2
#102
edyoshikun
closed
10 months ago
12
Deskew configuration file's `px_to_scan_ratio` parameter is redundant with scale metadata
#101
talonchandler
opened
1 year ago
0
replace the np.rot90 with affine transforms in `apply_affine()`
#100
edyoshikun
closed
10 months ago
1
Move logger config to mantis/__init__.py and rename to `mantis`
#99
ieivanov
closed
1 year ago
0
Manual "autoexposure": Apply per-well exposure time and laser power from file
#98
ieivanov
closed
1 year ago
4
Change default for deskew to YX and create_empty_zarr dtype
#97
edyoshikun
closed
1 year ago
5
Plot bleaching estimates with correct time and/or per volume units
#96
talonchandler
opened
1 year ago
2
Extend Ls scan range to cover the LF FOV
#95
ieivanov
closed
1 year ago
0
Affine scaling fix
#94
talonchandler
closed
1 year ago
0
Replacing global variables with scale metadata
#93
edyoshikun
closed
1 year ago
0
Should the output and config CLI calls have a default option?
#92
edyoshikun
closed
1 year ago
3
Restrict the estimate phase to fluor affine z-registration to theoretical microscope values to return proper voxel values.
#91
edyoshikun
closed
1 year ago
1
Modify global variables in estimate affine
#90
edyoshikun
closed
1 year ago
0
Better mantis acquisition cleanup
#89
ieivanov
closed
1 year ago
0
Switch LF z_step to units of sample-space micrometers
#88
ieivanov
closed
1 year ago
0
`ls_slice_settings.z_step` and `lf_slice_settings.z_step` use inconsistent scales
#87
talonchandler
closed
1 year ago
0
Update scale metadata
#86
edyoshikun
closed
1 year ago
1
Need a function to update the scale metadata from our datastores
#85
edyoshikun
closed
1 year ago
0
Need a pipeline to easily append new channels to existing stores
#84
edyoshikun
opened
1 year ago
0
Cropping the images to the largest area after applying the affine transformation
#83
edyoshikun
closed
10 months ago
0
Switch LS SliceSettings units to micrometers
#82
ieivanov
closed
1 year ago
0
Abort stalled acquisitions
#81
ieivanov
closed
1 year ago
1
Update MM version
#80
ieivanov
closed
1 year ago
1
Update KIM101 compensation factor
#79
ieivanov
closed
1 year ago
0
WIP: Abort stalled acquisitions
#78
ieivanov
closed
1 year ago
0
Cannot open two instances of micromanager
#77
edyoshikun
opened
1 year ago
0
Switch to using `pathlib` for path handling in `acq_engine`
#76
ieivanov
closed
1 year ago
0
Standardize CLI
#75
talonchandler
closed
1 year ago
5
Improve autofocus reengagement
#74
ieivanov
closed
1 year ago
0
Validate acquisition settings
#73
ieivanov
closed
1 year ago
6
WIP `dataclass` to `BaseModel` migration
#72
talonchandler
closed
1 year ago
1
All CLI calls read from zarr
#71
talonchandler
closed
1 year ago
0
Save HCS position label in NDTiff dataset axes
#70
ieivanov
closed
1 year ago
5
Update recommended sampling in the LS and LF remote refocus paths
#69
ieivanov
closed
1 year ago
0
Rename `settings` files to `config` files and clean up `examples` folders
#68
ieivanov
opened
1 year ago
0
Fix_deskew_utils
#67
edyoshikun
closed
1 year ago
1
Add tests for mantis acquisition engine
#66
ieivanov
opened
1 year ago
0
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