API

nd2dim(path_nd2)

Returns dim of the file in (x, y, z, t, c)

Arguments

• path_nd2: .nd2 file to read
• verbose: if true, print out the dimensions

nd2read(path_nd2; ch=1, t=1)

Read the image at ch and t

Arguments

• path_nd2: .nd2 file to read
• ch: ch to read. First ch: 1
• t: time point to read. Can be multiple. First t: 1

nd2preview(path_nd2; ch=1, return_data=false, z_crop=nothing)

Preview MIP of first, middle, and last time points in the .nd2 file

Arguments

• path_nd2: .nd2 file to read
• ch: ch to use. Default: 1 (first ch)
• return_data: if true returns the 3 images as array
• z_crop: selecting z range to use. e.g. 3:15 then only use slice 3 to 15

nd2preview_crop(stack::Array; θ, x_crop=nothing, y_crop=nothing,
    z_crop=nothing)

Preview MIP of rotatation and x, y, z cropping

Arguments

• stack: array (e.g. returned from nd2preview with return_data=true)

containing 3 stacks

• θ: yaw angle (lateral rotation)
• x_crop: range of x to use
• y_crop: range of y to use
• z_crop: range of z to use

nd2_to_mhd(path_nd2, path_save,
    spacing_lat, spacing_axi, generate_MIP::Bool;
    θ=nothing, x_crop::Union{Nothing, UnitRange{Int64}}=nothing,
    y_crop::Union{Nothing, UnitRange{Int64}}=nothing,
    z_crop::Union{Nothing, UnitRange{Int64}}=nothing, chs::Array{Int}=[1],
    MHD_dir_name="MHD", MIP_dir_name="MIP")

Saves nd2 into MHD files after rotating and cropping. Rotation is skipped if θ is set to nothing.

Arguments

• path_nd2: path of .nd2 file to use
• path_save: path of .h5 file to save
• spacing_lat: lateral spacing (for logging)
• spacing_axi: axial spacing (for logging)
• generate_MIP: if true, save MIP in as preview
• θ: yaw angle (lateral rotation, radian). nothing if no rotation
• x_crop: x range to use. Full range if nothing
• y_crop: y range to use. Full range if nothing
• z_crop: z range to use. Full range if nothing
• chs: ch to use
• MHD_dir_name: name of the subfolder to save MHD files
• MIP_dir_name: name of the subfolder to save MIP files

nd2_to_h5(path_nd2, path_save, spacing_lat, spacing_axi; θ=nothing,
    x_crop::Union{Nothing, UnitRange{Int64}}=nothing,
    y_crop::Union{Nothing, UnitRange{Int64}}=nothing,
    z_crop::Union{Nothing, UnitRange{Int64}}=nothing, chs::Array{Int}=[1])

Saves nd2 into HDF5 file after rotating and cropping. Rotation is skipped if θ is set to nothing. Note: indexing is 1 based. Array axis is in the following order: [x, y, z, t, c]. HDF5 file is chunked with: (x size, y size, z size, 1, 1, 1)

Arguments

• path_nd2: path of .nd2 file to use
• path_save: path of .h5 file to save
• spacing_lat: lateral spacing (for logging)
• spacing_axi: axial spacing (for logging)
• θ: yaw angle (lateral rotation, rauab). nothing if no rotation
• x_crop: x range to use. Full range if nothing
• y_crop: y range to use. Full range if nothing
• z_crop: z range to use. Full range if nothing
• chs: ch to use