To think about, and see whether we want to invest resources in this repo and where:
Flat-field correction
Our own
Option 1: we implement the flat field correction here. (division by gaussian blur, big median projection for instance). On the plus side, we don't need to depend on whether the Operetta system managed to compute a flat field reference. On the minus side this could be less great than what is done by the Operetta machine.
Use Perkin Elmer's one
Option 2: we use our reverse engineered understand of the flat field correction (is it a multiplicative or an additive correction ?), see https://forum.image.sc/t/how-to-use-illumination-correction-file-from-perkin-elmer-operetta-microscope-outside-of-harmony-in-imagej-or-cellprofiler-instead/31650/7 . The problem I see with that is that the flat field correction is sometimes not done by Operetta and then that's a pain
Better stitching
Challenges: make it work (= not fail too much) with missing features. Support all dimensional cases (T, Z)
Use Grid collection stitching (cf @lacan 's script which is somewhere)
Could be done here, with the data being mostly ImagePlus
Use BigStitcher
Needs to be done rather outside of this repo by using a BDV dataset
Better Export
Export as pyramidal representation ( OME TIFF for instance ) (#20)
Fix memory limitation
cf #8
Could be done with a BDV dataset
Other
Include the script that merge objects based on connected fields (cf @lacan's script somewhere)
To think about, and see whether we want to invest resources in this repo and where:
Flat-field correction
Our own
Option 1: we implement the flat field correction here. (division by gaussian blur, big median projection for instance). On the plus side, we don't need to depend on whether the Operetta system managed to compute a flat field reference. On the minus side this could be less great than what is done by the Operetta machine.
Use Perkin Elmer's one
Option 2: we use our reverse engineered understand of the flat field correction (is it a multiplicative or an additive correction ?), see https://forum.image.sc/t/how-to-use-illumination-correction-file-from-perkin-elmer-operetta-microscope-outside-of-harmony-in-imagej-or-cellprofiler-instead/31650/7 . The problem I see with that is that the flat field correction is sometimes not done by Operetta and then that's a pain
Better stitching
Challenges: make it work (= not fail too much) with missing features. Support all dimensional cases (T, Z)
Use Grid collection stitching (cf @lacan 's script which is somewhere)
Could be done here, with the data being mostly ImagePlus
Use BigStitcher
Needs to be done rather outside of this repo by using a BDV dataset
Better Export
Export as pyramidal representation ( OME TIFF for instance ) (#20)
Fix memory limitation
cf #8
Could be done with a BDV dataset
Other
Include the script that merge objects based on connected fields (cf @lacan's script somewhere)