czbiohub-sf shrimPy issues

czbiohub-sf / shrimPy

shrimPy: Smart High-throughput Robust Imaging & Measurement in Python

BSD 3-Clause "New" or "Revised" License

7 stars 1 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Rename `mantis` to `shrimpy`

#147 talonchandler opened 4 days ago
0
GPU deskew

#146 talonchandler opened 1 week ago
0
CLI for concatenating zarr stores

#145 edyoshikun opened 1 week ago
0
Hardcoded focus finding variables in stabilization algorithm

#144 edyoshikun opened 1 week ago
3
Apply_affine should allow custom target channels rather than copying all

#143 edyoshikun opened 1 week ago
0
migrating update scale metadata utility to iohub

#142 aaronalvarezcz opened 1 week ago
0
Mappings from physical components (phase,retardance,orientation) to HSV /JCh

#141 edyoshikun closed 1 week ago
5
Slurmkit copy n paste

#140 edyoshikun opened 4 weeks ago
1
Acquisition: add check for sufficient disk space

#139 ieivanov opened 1 month ago
0
Acquisition engine fixes

#138 ieivanov closed 1 month ago
0
Methods to stitch a position grid

#137 ieivanov opened 2 months ago
0
Registration: existing plugin

#136 ziw-liu opened 3 months ago
0
Methods to stitch a position grid array

#135 ieivanov closed 1 week ago
2
Fix t_idx and additional channels

#134 edyoshikun closed 1 week ago
2
Cannot apply affine transform

#133 ziw-liu closed 1 week ago
1
Editable installation in CONTRIBUTING.md

#132 ziw-liu closed 4 months ago
0
PSF measurement routine

#131 ieivanov closed 1 week ago
1
PSF measurement, simulation, and deconvolution

#130 talonchandler opened 5 months ago
0
GPU peak detection with torch

#129 ziw-liu closed 5 months ago
1
XY and Z drift stabilization; replaces #108

#128 ieivanov closed 1 week ago
5
bump iohub dependencies

#127 edyoshikun opened 5 months ago
2
Registration: in `estimate_affine` check that selected points are not outside of the data volume when in grid mode

#126 ieivanov opened 5 months ago
0
Registration: check how `apply_affine` handles positions will all nans or zeros

#125 ieivanov opened 5 months ago
0
Registration: find better cropping algorithm

#124 ieivanov opened 5 months ago
0
Refactor and unify reconstruction calls

#123 ieivanov opened 5 months ago
0
CLI renaming

#122 ieivanov opened 5 months ago
0
Registration: rename `target` to `fixed` and `source` to `moving` to match convention in other image registration pipelines

#121 ieivanov opened 5 months ago
0
Remove white spaces in readme

#120 ieivanov closed 5 months ago
0
Update readme with link to preprint

#119 ieivanov closed 5 months ago
2
Registration refator

#118 ieivanov closed 5 months ago
0
Update readme

#117 mattersoflight closed 6 months ago
0
Update readme.md

#116 ieivanov closed 6 months ago
0
Better cropping of registered datasets

#115 ieivanov closed 5 months ago
0
Registration `source` and `target` images should be renamed to `moving` and `fixed`

#114 ieivanov closed 5 months ago
1
`update-scale-metadata` CLI call needs a docstring

#113 ieivanov opened 7 months ago
1
Merging the PRs

#112 edyoshikun opened 7 months ago
1
Slurmkit scripts slowing down the I/O

#111 edyoshikun opened 7 months ago
0
Mantis processing pipeline

#110 edyoshikun opened 7 months ago
1
Denoise and illumination background correction

#109 edyoshikun opened 7 months ago
0
XY and Z drift stabilization

#108 edyoshikun closed 5 months ago
1
function to merge multiple stores

#107 edyoshikun closed 1 week ago
1
Segmentation (no CLI)

#106 edyoshikun opened 7 months ago
0
Only move stage when going to different position

#105 ieivanov closed 8 months ago
0
More robust acquisition abort

#104 ieivanov closed 8 months ago
0
Z-drift and XY stabilization

#103 edyoshikun closed 7 months ago
3
Registration V2

#102 edyoshikun closed 5 months ago
12
Deskew configuration file's `px_to_scan_ratio` parameter is redundant with scale metadata

#101 talonchandler opened 9 months ago
0
replace the np.rot90 with affine transforms in `apply_affine()`

#100 edyoshikun closed 5 months ago
1
Move logger config to mantis/__init__.py and rename to `mantis`

#99 ieivanov closed 10 months ago
0
Manual "autoexposure": Apply per-well exposure time and laser power from file

#98 ieivanov closed 9 months ago
4