GitHub - m-albert/preprocessing

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 8 Commits
#pipeline_opt2.py#		#pipeline_opt2.py#
README		README
affine_fit.py		affine_fit.py
beads.py		beads.py
calcNormalizationRatios.py		calcNormalizationRatios.py
configuration.py		configuration.py
configuration_beads.py		configuration_beads.py
configuration_template.py		configuration_template.py
delme.py		delme.py
execute-linux.sh		execute-linux.sh
execute-windows.bat		execute-windows.bat
execute.sh		execute.sh
extras.py		extras.py
filters.py		filters.py
fusion.py		fusion.py
h5totif.h5.py		h5totif.h5.py
imports.py		imports.py
initialTransformTemplate.txt		initialTransformTemplate.txt
parameterExplanation.txt		parameterExplanation.txt
parameterTemplate.txt		parameterTemplate.txt
pipeline.py		pipeline.py
pipeline2.py		pipeline2.py
pipeline_nils.py		pipeline_nils.py
pipeline_nobeads.py		pipeline_nobeads.py
pipeline_opt.py		pipeline_opt.py
pipeline_opt2.py		pipeline_opt2.py
pipeline_opt2.py.save		pipeline_opt2.py.save
ransac.py		ransac.py
ransac_old.py		ransac_old.py
shear.py		shear.py
shear2.py		shear2.py
shear_aut.py		shear_aut.py
shear_aut2_testcall.txt		shear_aut2_testcall.txt
shear_backup.py		shear_backup.py
shear_new.py		shear_new.py
shear_test.py		shear_test.py
test.py		test.py
tifffile.py		tifffile.py
tmplog.txt		tmplog.txt
transformations.py		transformations.py

Repository files navigation

PIPELINE FOR PREPROCESSING MUVI-SPIM DATA
AUTHOR: MARVIN ALBERT (marvin.albert@gmail.com)

input:
    bead files
    data timepoints
    
output:
    (bead alignment parameters)
    fused stack
    
usage:
- define parameters in configuration.py (template with explanations available in main folder)
- run the pipeline:
    linux:
        run execute-linux.sh pathToConfigurationFile
    windows:
        specifiy <pathToConfigurationFile> in execute-windows.bat and execute

dependencies contained in the binary (anaconda python):
1) python 2.6
2) numpy
3) scipy
5) SimpleITK
6) elastix

comments:
- alignment parameters are only calculated once and placed in out/pipe
- approx. 10GB of RAM required for full fusion of 2*2 views
- currently not fully supporting imaging settings other than: 2 opposing cameras and 2 orthogonal rotational views
- further settings regarding the image based alignment are defined in parameterTemplate.txt and initialTransformTemplate.txt

to do:
- save obtained parameters and make them usable for next run (add option to indicate wether to use old params or nor)
- generalize weights for final fusion (only for 0 and 90 degrees at the moment)
- handle case without rotation
- determine exact meaning of convergence criterium in elastix
- write correct meta data to tiff files
- copy data over network while computing (optimize for normal use mode and enable ssh support for cluster queing when directories cannot be mounted) (command line scp client for windows: http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html)
- dont automatically overwrite
- otsu threshold for bead segmentation