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dexp documentation
dexp documentation

Getting started

  • Install
  • Contact us

How-to guides

  • Converting to our file format
  • Visualizing your data
  • Processing a multi-view dataset using DEXP CLI
  • Implementing your own processing pipeline

Commands

  • Image processing
  • Video rendering

API

  • API
    • dexp.datasets
      • dexp.datasets.base_dataset
      • dexp.datasets.clearcontrol_dataset
      • dexp.datasets.joined_dataset
      • dexp.datasets.ome_dataset
      • dexp.datasets.open_dataset
      • dexp.datasets.operations
        • dexp.datasets.operations.background
        • dexp.datasets.operations.copy
        • dexp.datasets.operations.crop
        • dexp.datasets.operations.deconv
        • dexp.datasets.operations.denoise
        • dexp.datasets.operations.deskew
        • dexp.datasets.operations.extract_psf
        • dexp.datasets.operations.fromraw
        • dexp.datasets.operations.fuse
        • dexp.datasets.operations.generic
        • dexp.datasets.operations.histogram
        • dexp.datasets.operations.projrender
        • dexp.datasets.operations.register
        • dexp.datasets.operations.segment
        • dexp.datasets.operations.stabilize
        • dexp.datasets.operations.tiff
        • dexp.datasets.operations.view
      • dexp.datasets.stack_iterator
      • dexp.datasets.synthetic_datasets
        • dexp.datasets.synthetic_datasets.binary_blobs
        • dexp.datasets.synthetic_datasets.dexp_dataset
        • dexp.datasets.synthetic_datasets.multiview_data
        • dexp.datasets.synthetic_datasets.nuclei_background_data
      • dexp.datasets.tiff_dataset
      • dexp.datasets.zarr_dataset
    • dexp.optics
      • dexp.optics.psf
        • dexp.optics.psf.microscope_psf
        • dexp.optics.psf.standard_psfs
    • dexp.processing
      • dexp.processing.color
        • dexp.processing.color.blend
        • dexp.processing.color.border
        • dexp.processing.color.cairo_utils
        • dexp.processing.color.colormap
        • dexp.processing.color.conversions
        • dexp.processing.color.crop_resize_pad
        • dexp.processing.color.insert
        • dexp.processing.color.projection
        • dexp.processing.color.projection_legend
        • dexp.processing.color.scale_bar
        • dexp.processing.color.time_stamp
      • dexp.processing.crop
        • dexp.processing.crop.background
        • dexp.processing.crop.demo
          • dexp.processing.crop.demo.demo_rep_crop
        • dexp.processing.crop.representative_crop
      • dexp.processing.deconvolution
        • dexp.processing.deconvolution.admm_deconvolution
        • dexp.processing.deconvolution.admm_utils
        • dexp.processing.deconvolution.blind_deconvolution
        • dexp.processing.deconvolution.inversion_deconvolution
        • dexp.processing.deconvolution.lr_deconvolution
      • dexp.processing.denoising
        • dexp.processing.denoising.butterworth
        • dexp.processing.denoising.demo
          • dexp.processing.denoising.demo.demo_2D_butterworth
          • dexp.processing.denoising.demo.demo_2D_gaussian
          • dexp.processing.denoising.demo.demo_3D_butterworth
          • dexp.processing.denoising.demo.demo_noise
        • dexp.processing.denoising.gaussian
        • dexp.processing.denoising.j_invariance
        • dexp.processing.denoising.metrics
        • dexp.processing.denoising.noise
      • dexp.processing.deskew
        • dexp.processing.deskew.classic_deskew
        • dexp.processing.deskew.utils
        • dexp.processing.deskew.yang_deskew
      • dexp.processing.equalise
        • dexp.processing.equalise.equalise_intensity
      • dexp.processing.filters
        • dexp.processing.filters.butterworth_filter
        • dexp.processing.filters.fft_convolve
        • dexp.processing.filters.kernels
          • dexp.processing.filters.kernels.butterworth
          • dexp.processing.filters.kernels.gaussian
          • dexp.processing.filters.kernels.wiener
          • dexp.processing.filters.kernels.wiener_butterworth
        • dexp.processing.filters.sobel_filter
      • dexp.processing.fusion
        • dexp.processing.fusion.dct_fusion
        • dexp.processing.fusion.dft_fusion
        • dexp.processing.fusion.tg_fusion
      • dexp.processing.interpolation
        • dexp.processing.interpolation.warp
      • dexp.processing.morphology
        • dexp.processing.morphology.component_tree
        • dexp.processing.morphology.utils
      • dexp.processing.multiview_lightsheet
        • dexp.processing.multiview_lightsheet.deconvolution
        • dexp.processing.multiview_lightsheet.fusion
          • dexp.processing.multiview_lightsheet.fusion.basefusion
          • dexp.processing.multiview_lightsheet.fusion.mvsols
          • dexp.processing.multiview_lightsheet.fusion.simview
      • dexp.processing.optimization
        • dexp.processing.optimization.grid_search
      • dexp.processing.registration
        • dexp.processing.registration.model
          • dexp.processing.registration.model.model_io
          • dexp.processing.registration.model.pairwise_registration_model
          • dexp.processing.registration.model.sequence_registration_model
          • dexp.processing.registration.model.translation_registration_model
          • dexp.processing.registration.model.warp_registration_model
        • dexp.processing.registration.sequence
        • dexp.processing.registration.sequence_proj
        • dexp.processing.registration.translation_2d
        • dexp.processing.registration.translation_nd
        • dexp.processing.registration.translation_nd_proj
        • dexp.processing.registration.warp_multiscale_nd
        • dexp.processing.registration.warp_nd
      • dexp.processing.remove_beads
        • dexp.processing.remove_beads.beadsremover
      • dexp.processing.restoration
        • dexp.processing.restoration.aap_correction
        • dexp.processing.restoration.clean_dark_regions
        • dexp.processing.restoration.dehazing
        • dexp.processing.restoration.lipshitz_correction
      • dexp.processing.segmentation
        • dexp.processing.segmentation.watershed
      • dexp.processing.utils
        • dexp.processing.utils.apply
        • dexp.processing.utils.blend_images
        • dexp.processing.utils.center_of_mass
        • dexp.processing.utils.element_wise_affine
        • dexp.processing.utils.fit_shape
        • dexp.processing.utils.linear_solver
        • dexp.processing.utils.mkl_util
        • dexp.processing.utils.nan_to_zero
        • dexp.processing.utils.nd_slice
        • dexp.processing.utils.normalise
        • dexp.processing.utils.pad
        • dexp.processing.utils.projection_generator
        • dexp.processing.utils.scatter_gather_i2i
        • dexp.processing.utils.scatter_gather_i2v
    • dexp.utils
      • dexp.utils.backends
        • dexp.utils.backends.backend
        • dexp.utils.backends.best_backend
        • dexp.utils.backends.cupy_backend
        • dexp.utils.backends.numpy_backend
      • dexp.utils.config
      • dexp.utils.dask
      • dexp.utils.fft
      • dexp.utils.lock
      • dexp.utils.misc
      • dexp.utils.robocopy
      • dexp.utils.slicing
      • dexp.utils.speed_test
      • dexp.utils.testing
        • dexp.utils.testing.testing
      • dexp.utils.timeit
    • dexp.video
      • dexp.video.blend
      • dexp.video.crop_resize_pad
      • dexp.video.overlay
    • dexp.volumerender
      • dexp.volumerender.quaternion
      • dexp.volumerender.transform_matrices
      • dexp.volumerender.volumerender

dexp.processing.deskew

Modules

dexp.processing.deskew.classic_deskew(image, ...)

Classic Deskewing.

dexp.processing.deskew.utils

dexp.processing.deskew.yang_deskew(image, ...)

'Yang' Deskewing as done in Yang et al. 2019 ( https://www.biorxiv.org/content/10.1101/2020.09.22.309229v2 ).
Next
dexp.processing.deskew.classic_deskew
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