czbiohub-sf/shrimPy

Issues

• CLI renaming

  #122 opened 3 months ago by ieivanov
  0

• `update-scale-metadata` CLI call needs a docstring

  #113 opened 4 months ago by ieivanov
  1

• Bug if pixel_size = 1.0 um

  #162 opened 4 months ago by ahillsley
  0

• Name our new image processing library

  #151 opened 4 months ago by talonchandler
  6

• ShrimPy need to be updated to Pydantic v2

  #159 opened 4 months ago by tayllatheodoro
  0

• missing packages to run the acquisition

  #157 opened 4 months ago by edyoshikun
  1

• Default number of workers for multiprocessing

  #62 opened 5 months ago by ieivanov
  6

• Merging the PRs

  #112 opened 5 months ago by edyoshikun
  1

• bump iohub dependencies

  #127 opened 5 months ago by edyoshikun
  3

• Hardcoded focus finding variables in stabilization algorithm

  #144 opened 6 months ago by edyoshikun
  3

• Apply_affine should allow custom target channels rather than copying all

  #143 opened 6 months ago by edyoshikun
  0

• Cannot apply affine transform

  #133 opened 6 months ago by ziw-liu
  1

• Acquisition: add check for sufficient disk space

  #139 opened 8 months ago by ieivanov
  0

• Registration: existing plugin

  #136 opened 9 months ago by ziw-liu
  0

• Better cropping of registered datasets

  #115 opened a year ago by ieivanov
  0

• Cropping the images to the largest area after applying the affine transformation

  #83 opened a year ago by edyoshikun
  0

• replace the np.rot90 with affine transforms in `apply_affine()`

  #100 opened a year ago by edyoshikun
  1

• Mantis processing pipeline

  #110 opened a year ago by edyoshikun
  1

• Registration `source` and `target` images should be renamed to `moving` and `fixed`

  #114 opened a year ago by ieivanov
  1

• Registration: in `estimate_affine` check that selected points are not outside of the data volume when in grid mode

  #126 opened a year ago by ieivanov
  0

• Registration: find better cropping algorithm

  #124 opened a year ago by ieivanov
  0

• Registration: check how `apply_affine` handles positions will all nans or zeros

  #125 opened a year ago by ieivanov
  0

• Refactor and unify reconstruction calls

  #123 opened a year ago by ieivanov
  0

• Registration: rename `target` to `fixed` and `source` to `moving` to match convention in other image registration pipelines

  #121 opened a year ago by ieivanov
  0

• Slurmkit scripts slowing down the I/O

  #111 opened a year ago by edyoshikun
  0

• Rename `settings` files to `config` files and clean up `examples` folders

  #68 opened a year ago by ieivanov
  0

• Cannot open two instances of micromanager

  #77 opened a year ago by edyoshikun
  0

• Control Vortran lasers through `copylot`

  #45 opened a year ago by edyoshikun
  2

• Plot bleaching estimates with correct time and/or per volume units

  #96 opened a year ago by talonchandler
  2

• Deskew configuration file's `px_to_scan_ratio` parameter is redundant with scale metadata

  #101 opened a year ago by talonchandler
  0

• Mantis uses root logger which captures events from external modules

  #61 opened a year ago by ieivanov
  0

• Prime BSI Express camera has high column noise

  #51 opened a year ago by ieivanov
  1

• Restrict the estimate phase to fluor affine z-registration to theoretical microscope values to return proper voxel values.

  #91 opened a year ago by edyoshikun
  1

• Modify global variables in estimate affine

  #90 opened a year ago by edyoshikun
  0

• Should the output and config CLI calls have a default option?

  #92 opened a year ago by edyoshikun
  3

• `ls_slice_settings.z_step` and `lf_slice_settings.z_step` use inconsistent scales

  #87 opened a year ago by talonchandler
  0

• Need a function to update the scale metadata from our datastores

  #85 opened a year ago by edyoshikun
  0

• Need a pipeline to easily append new channels to existing stores

  #84 opened a year ago by edyoshikun
  0

• mantis acquisitions save incorrect `z-step_um` metadata

  #58 opened a year ago by talonchandler
  2

• Acquisition finishes but fails to cleanup

  #41 opened a year ago by edyoshikun
  4

• Revert back to checking if acq is finished based on image_saved_fn callback

  #64 opened a year ago by ieivanov
  0

• Unify CLI call signatures

  #65 opened a year ago by ieivanov
  4

• Add documentation on mantis CLI options

  #56 opened a year ago by ieivanov
  1

• Convert to zarr as an initial analysis step

  #42 opened a year ago by talonchandler
  5

• Add more testing for missing variables for Channel Settings.

  #40 opened a year ago by edyoshikun
  9

• Merge slurm deskew with `mantis deskew` CLI call

  #57 opened a year ago by ieivanov
  1

• IPC diagram

  #43 opened 2 years ago by ziw-liu
  1

• Add tests for mantis acquisition engine

  #66 opened a year ago by ieivanov
  0

• Develop image-based autofocus for LF arm

  #63 opened a year ago by ieivanov
  0

• Mantis acq fails silently if wrong config group / config name is provided

  #60 opened a year ago by ieivanov
  0