Index

A

aicsimageprocessing (module) aicsimageprocessing.alignMajor (module) aicsimageprocessing.backgroundCrop (module) aicsimageprocessing.backgroundSub (module) aicsimageprocessing.bin (module) aicsimageprocessing.bin.make_atlas (module) aicsimageprocessing.bin.make_thumbnail (module) aicsimageprocessing.crop_img (module) aicsimageprocessing.flip (module) aicsimageprocessing.imgCenter (module) aicsimageprocessing.imgToCoords (module) aicsimageprocessing.imgToProjection (module) aicsimageprocessing.imshow (module)

aicsimageprocessing.isosurfaceGenerator (module) aicsimageprocessing.normalization (module) aicsimageprocessing.resize (module) aicsimageprocessing.rigidAlignment (module) aicsimageprocessing.sdfGenerator (module) aicsimageprocessing.segmentation (module) aicsimageprocessing.segmentation.nucleusSegmentation (module) aicsimageprocessing.textureAtlas (module) aicsimageprocessing.thumbnailGenerator (module) aicsimageprocessing.transformation (module) align_major() (in module aicsimageprocessing.alignMajor) angle_between() (in module aicsimageprocessing.alignMajor) Args (class in aicsimageprocessing.bin.make_atlas) (class in aicsimageprocessing.bin.make_thumbnail)

B

background_sub() (in module aicsimageprocessing.backgroundSub)

C

cart2sph() (in module aicsimageprocessing.imgToCoords) cell_rigid_deregistration() (in module aicsimageprocessing.rigidAlignment) cell_rigid_registration() (in module aicsimageprocessing.rigidAlignment) center() (in module aicsimageprocessing.imgCenter) combine_mask_sdf() (in module aicsimageprocessing.sdfGenerator)

combine_sdf() (in module aicsimageprocessing.sdfGenerator) create_projection() (in module aicsimageprocessing.thumbnailGenerator) crop() (in module aicsimageprocessing.backgroundCrop) crop_all() (in module aicsimageprocessing.imgCenter) crop_img() (in module aicsimageprocessing.crop_img) (in module aicsimageprocessing.rigidAlignment)

F

fill_nucleus_segmentation() (in module aicsimageprocessing.segmentation.nucleusSegmentation)

flip() (in module aicsimageprocessing.flip) flipdims() (in module aicsimageprocessing.rigidAlignment)

G

generate_atlas() (aicsimageprocessing.textureAtlas.TextureAtlas method) generate_mesh() (in module aicsimageprocessing.isosurfaceGenerator) generate_texture_atlas() (in module aicsimageprocessing.textureAtlas) get_align_angles() (in module aicsimageprocessing.alignMajor) get_center_moves() (in module aicsimageprocessing.imgCenter) get_center_of_mass() (in module aicsimageprocessing.rigidAlignment) get_channel() (in module aicsimageprocessing.rigidAlignment)

get_edges() (in module aicsimageprocessing.backgroundCrop) get_flipdims() (in module aicsimageprocessing.rigidAlignment) get_flips() (in module aicsimageprocessing.flip) get_major_angle() (in module aicsimageprocessing.rigidAlignment) get_major_minor_axis() (in module aicsimageprocessing.alignMajor) get_metadata() (aicsimageprocessing.textureAtlas.TextureAtlasGroup method) get_module_version() (in module aicsimageprocessing) get_rigid_reg_stats() (in module aicsimageprocessing.rigidAlignment)

I

img_to_coords() (in module aicsimageprocessing.imgToCoords)

imgtoprojection() (in module aicsimageprocessing.imgToProjection) imshow() (in module aicsimageprocessing.imshow)

K

keep_connected_components() (in module aicsimageprocessing.segmentation.nucleusSegmentation)

M

main() (in module aicsimageprocessing.bin.make_atlas) (in module aicsimageprocessing.bin.make_thumbnail) make_one_thumbnail() (in module aicsimageprocessing.thumbnailGenerator) make_thumbnail() (aicsimageprocessing.thumbnailGenerator.ThumbnailGenerator method)

make_vtkpolydata() (in module aicsimageprocessing.sdfGenerator) make_vtkvolume() (in module aicsimageprocessing.sdfGenerator) mask_normalization() (in module aicsimageprocessing.normalization) matproj() (in module aicsimageprocessing.imgToProjection) Mesh (class in aicsimageprocessing.isosurfaceGenerator)

N

normalize_channel() (in module aicsimageprocessing.normalization)

normalize_img() (in module aicsimageprocessing.normalization)

O

obj_to_sdf() (in module aicsimageprocessing.sdfGenerator)

P

pad_to_com() (in module aicsimageprocessing.rigidAlignment)

pad_to_position() (in module aicsimageprocessing.rigidAlignment)

R

rescale() (in module aicsimageprocessing.normalization) resize() (in module aicsimageprocessing.resize)

resize_cyx_image() (in module aicsimageprocessing.thumbnailGenerator) resize_to() (in module aicsimageprocessing.resize)

S

save() (aicsimageprocessing.textureAtlas.TextureAtlasGroup method) save_as_obj() (aicsimageprocessing.isosurfaceGenerator.Mesh method) save_mesh() (in module aicsimageprocessing.sdfGenerator)

save_mesh_vtk() (in module aicsimageprocessing.sdfGenerator) save_sdf() (in module aicsimageprocessing.sdfGenerator) sph2cart() (in module aicsimageprocessing.imgToCoords) subtract_noise_floor() (in module aicsimageprocessing.thumbnailGenerator)

T

TextureAtlas (class in aicsimageprocessing.textureAtlas) TextureAtlasDims (class in aicsimageprocessing.textureAtlas)

TextureAtlasGroup (class in aicsimageprocessing.textureAtlas) ThumbnailGenerator (class in aicsimageprocessing.thumbnailGenerator) transform() (in module aicsimageprocessing.transformation)

U

unit_vector() (in module aicsimageprocessing.alignMajor)

V

volume_to_obj() (in module aicsimageprocessing.sdfGenerator) volume_to_sdf() (in module aicsimageprocessing.sdfGenerator)

vtk_iterate_cells() (in module aicsimageprocessing.sdfGenerator) vtkImg3dToNumpyArray() (in module aicsimageprocessing.sdfGenerator)