toolbox package#

Submodules#

toolbox.imagePreProcessing module#

Created on Sun Feb 28 13:44:47 2021

@author: marcnol

  • loads a list of images from a folder

  • re-scales exposures

  • removes inhomogeneous background

  • adjusts image levels

  • saves output in TIF

Steps:

  • defines run_parameters

  • gets list of images in folder using wildcard, *tif by default

  • loads iteratively images and applies operations described above

  • saves output

toolbox.imagePreProcessing.lauch_dask_scheduler(requested_nb_nodes, maximum_load=0.6, memory_per_worker=2000)#
toolbox.imagePreProcessing.main()#
toolbox.imagePreProcessing.parse_arguments()#

toolbox.imageSegmentSpots module#

Created on Mon Mar 8 16:54:49 2021

@author: marcnol

  • loads a list of images from a folder

  • segments image in 3D

  • saves output in TIF

Steps:

  • defines run_parameters

  • loads iteratively images and segments volumes

  • saves output

toolbox.imageSegmentSpots.main()#
toolbox.imageSegmentSpots.parse_arguments()#

toolbox.runHiM_cluster module#

Created on Fri May 7 19:28:21 2021

@author: marcnol

Lauches slurm srun job

In the command line, run as $ runHiM_cluster.py

toolbox.runHiM_cluster.main()#
toolbox.runHiM_cluster.read_arguments()#

Module contents#