Precomputed manager

class library.image_manipulation.precomputed_manager.NgPrecomputedMaker

Bases: object

Class to convert a tiff image stack to the precomputed neuroglancer format code from Seung lab

create_downsamples()

Downsamples the neuroglancer cloudvolume this step is needed to make the files viewable in neuroglancer

create_neuroglancer()

create the Seung lab cloud volume format from the image stack

create_neuroglancer_normalization()

Downsamples the neuroglancer cloudvolume this step is needed to make the files viewable in neuroglancer

get_file_information(INPUT, PROGRESS_DIR)

getting the information of files in the directory

Args:

INPUT (str): path to input directory

Returns:

str: name of the tif images corresponding to the section in the middle of the stack list: list of id and filename tuples for the files in the directory tuple: tuple of integers for the width,height and number of sections in the stack int: number of channels present in each tif files

get_scales()

returns the scanning resolution for a given animal. The scan resolution and sectioning thickness are retrived from the database. The resolution in the database is stored as micrometers (microns -um). But neuroglancer wants nanometers so we multipy by 1000

Returns:

list of converstion factors from pixel to micron for x,y and z