| Stable Release | Documentation | Build Status |
|---|---|---|
 |
 |
   |
Adds support for reading OME-TIFF files to the Images.jl platform. Allows fast and easy interfacing with high-dimensional data with nice labeled axes provided by AxisArrays.jl.
- Can open a wide-range of OMETIFF files with a special focus on correctness
- Supports memory-mapping to open large TIFF files quickly even on memory-constrained machines
- Spatial and temporal axes are annotated with units if available (like μm, s, etc)
- Channel and position axes use their original names
- Elapsed times are extracted and returned using the same labeled axes
- Important metadata is extracted and included in an easy to access format
OMETIFF.jl will be automatically installed when you use FileIO to open an OME-TIFF file. You can also install it by running the following in the Julia REPL:
] add OMETIFFjulia> using FileIO, Images
julia> img = load("/Users/tamasnagy/Downloads/66perc-h2o-vs-iso_1_MMStack.ome.tif")
Gray ImageMeta with:
data: 4-dimensional AxisArray{Gray{N0f16},4,...} with axes:
:y, 0.0 μm:0.6518 μm:666.7914000000001 μm
:x, 0.0 μm:0.6518 μm:666.7914000000001 μm
:time, 0.0 ms:15000.0 ms:405000.0 ms
:position, Symbol[:A5_Site_0, :A5_Site_1, :B5_Site_0, :B5_Site_1]
And data, a 1024×1024×28×4 reshape(reinterpret(Gray{N0f16}, ::Array{UInt16,6}), 1024, 1024, 28, 4) with eltype Gray{Normed{UInt16,16}}
properties:
Elapsed_Times: Unitful.Quantity{Float64,𝐓,Unitful.FreeUnits{(s,),𝐓,nothing}}[2.525 s 3.35 s 5.638 s 6.534 s; 15.398 s 16.195 s 18.743 s 19.506 s; … ; 390.389 s 391.154 s 393.282 s 393.984 s; 405.391 s 406.13 s 408.316 s 409.101 s]
Description: nd4 + nd8 in
julia> size(img) # lets get the dimensions
(1024, 1024, 28, 4)
julia> axisnames(img) # wait, but what do they correspond to?
(:y, :x, :time, :position)
julia> img[Axis{:position}(:A5_Site_1), Axis{:time}(2)]; # get the 2nd time point in position A5
julia> img["Elapsed_Times"][Axis{:position}(:A5_Site_1), Axis{:time}(2)] # get exact time when that slice was taken
16.195 s
julia> img["Description"] # get any notes embedded in the image
"nd4 + nd8 in"The image updates all the axes as we subset it. Observe that since we're grabbing 5x5x1x1 subset of the image, all the axes update to reflect this slice.
julia> using Unitful
julia> img[Axis{:y}(1:5), Axis{:x}(1:5), Axis{:time}(15000u"ms"), Axis{:position}(1)]
Gray ImageMeta with:
data: 2-dimensional AxisArray{Gray{N0f16},2,...} with axes:
:y, 0.0 μm:0.6518 μm:2.6072 μm
:x, 0.0 μm:0.6518 μm:2.6072 μm
And data, a 5×5 Array{Gray{N0f16},2} with eltype Gray{Normed{UInt16,16}}
properties:
Elapsed_Times: Quantity{Float64,𝐓,Unitful.FreeUnits{(s,),𝐓,nothing}}[2.525 s 3.35 s 5.638 s 6.534 s; 15.398 s 16.195 s 18.743 s 19.506 s; … ; 390.389 s 391.154 s 393.282 s 393.984 s; 405.391 s 406.13 s 408.316 s 409.101 s]
Description: nd4 + nd8 inTo quickly access the OME-XML stored inside a TIFF file, use the
OMETIFF.dump_omexml function:
julia> using OMETIFF
julia> println(OMETIFF.dump_omexml("test/testdata/singles/single-channel.ome.tif"))
<OME xmlns="https://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="https://www.w3.org/2001/XMLSchema-instance" Creator="OME Bio-Formats 5.2.2" UUID="urn:uuid:2bc2aa39-30d2-44ee-8399-c513492dd5de" xsi:schemaLocation="https://www.openmicroscopy.org/Schemas/OME/2016-06 https://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
<Image ID="Image:0" Name="single-channel.ome.tif">
<Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" SizeC="1" SizeT="1" SizeX="439" SizeY="167" SizeZ="1" Type="int8">
<Channel ID="Channel:0:0" SamplesPerPixel="1">
<LightPath/>
</Channel>
<TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1">
<UUID FileName="single-channel.ome.tif">urn:uuid:2bc2aa39-30d2-44ee-8399-c513492dd5de</UUID>
</TiffData>
</Pixels>
</Image>
</OME>