BioformatsLoader.jl

A julia package to load images using bioformats
Author ahnlabb
Popularity
6 Stars
Updated Last
4 Months Ago
Started In
February 2018

BioformatsLoader

Build Status

Coverage Status

codecov.io

Usage

Requires bioformats_package.jar

Pkg.clone("https://github.com/ahnlabb/BioformatsLoader.jl")
using BioformatsLoader
using JavaCall

bfpkg_path = "/path/to/bioformats_package.jar"

try
        JavaCall.init(["-ea", "-Xmx1024M", "-Djava.class.path=$bfpkg_path"])
end

To import the file file.msr you then do

image = bf_import("file.msr")

The variable image will contain an array of ImageMetadata, the data will be the type that the format specifies: Int8, UInt8, Int16, UInt16, Int32, UInt32, Float32, Float64 or Bool.