Microscope-Specific File Formats

Use Bio-Formats to import and read microscopy image data and metadata

Install the package BioFormatsLink to access the Bio-Formats library, a community-driven software tool for reading and writing over 140 file formats and their metadata. Then load the package:

In[1]:=

Needs["BioFormatsLink`"]

Import a NIfTI test file, a format developed by NIH (National Institutes of Health):

In[2]:=

data=Import

url

,"BioImageFormat"1,1;

Build a 3D volume from the imported series:

In[3]:=

ImageRotate[Image3D[data],180°]

Out[63]=

Download and unpack a ZIP-archived Leica LIF file of a mouse kidney section as provided by Jean-Yves Tinevez of the PFID Imagopole at the Institut Pasteur, Paris:

In[4]:=

filePath=FirstQuietExtractArchiveURLDownload

mouse-kidney

,$UserDocumentsDirectory,{ExtractArchive::filex},FirstFileNamesFileBaseName

mouse-kidney

<>".*",$UserDocumentsDirectory;

Import the first series of images as a 3D volume:

In[5]:=

mouseKidneyXYZ=Image3D[First@Import[filePath,{"BioImageFormat","ImageList",1}]/4095,"Bit16"];

View the stack of images:

In[6]:=

ManipulateImage3DSlices[mouseKidneyXYZ,z],{{z,18},1,25,1},

...



Out[6]=

Image metainformation such as the modality, the recording device, exposure time, etc. is usually stored in the metadata of an image file. Extract the plain metainformation as a list of rules:

In[7]:=

Import[filePath,{"BioImageFormat","OriginalMetaInformation"}]

Out[7]=

{{sizeX512,sizeY512,sizeZ25,sizeC4,sizeT1,thumbSizeX0,thumbSizeY0,pixelTypeuint16,bitsPerPixel16,imageCount100,dimensionOrderXYCZT,orderCertaintrue,rgbfalse,littleEndiantrue,interleavedfalse,indexedtrue,falseColortrue,metadataCompletetrue,seriesMetadata297 keys,thumbnailfalse},{sizeX512,sizeY512,sizeZ46,sizeC4,sizeT1,thumbSizeX0,thumbSizeY0,pixelTypeuint16,bitsPerPixel16,imageCount184,dimensionOrderXYCZT,orderCertaintrue,rgbfalse,littleEndiantrue,interleavedfalse,indexedtrue,falseColortrue,metadataCompletetrue,seriesMetadata299 keys,thumbnailfalse}}

Import the OME metainformation as an XML structure:

In[8]:=

xml=Import[filePath,{"BioImageFormat","OMEXMLMetaInformation"}];

A lot of information can be extracted from the metainformation, e.g. microscope and filter specifications, acquisition dates, data and channel encodings, etc. Extract voxel-related information of the first image series as a list of replacement rules:

In[9]:=

pixelRules=FirstCase[FirstCase[xml,XMLElement["Image",_,imgElems_List]imgElems,{},{3}],XMLElement["Pixels",pixelSpecs_,{___}]pixelSpecs,{},{1}]

Out[9]=

{BigEndianfalse,DimensionOrderXYCZT,IDPixels:0,Interleavedfalse,PhysicalSizeX1.5166340508806262,PhysicalSizeXUnitµm,PhysicalSizeY1.5166340508806262,PhysicalSizeYUnitµm,PhysicalSizeZ0.999928474358057,PhysicalSizeZUnitµm,SignificantBits16,SizeC4,SizeT1,SizeX512,SizeY512,SizeZ25,Typeuint16}

Construct the voxel size in the

and

directions as a list of quantities:

In[10]:=

voxelSize=Apply[Quantity,Replace[{{"PhysicalSizeX","PhysicalSizeXUnit"},{"PhysicalSizeY","PhysicalSizeYUnit"},{"PhysicalSizeZ","PhysicalSizeZUnit"}},pixelRules,{2}],{1}]

Out[10]=



1.5166340508806262

μm

1.5166340508806262

μm

0.999928474358057

μm



The first image series was acquired by stimulated emission depletion (STED). Extract the laser wavelengths used in this modality:

In[11]:=

laserRules=Cases[FirstCase[xml,XMLElement["Instrument",_,instElems_List]instElems,{},{3}],XMLElement["Laser",laserSpecs_,{___}]laserSpecs,{1}]

Out[11]=

{{IDLightSource:0:0,LaserMediumOther,TypeOther,Wavelength405.0,WavelengthUnitnm},{IDLightSource:0:1,LaserMediumOther,TypeOther,Wavelength458.0,WavelengthUnitnm},{IDLightSource:0:2,LaserMediumOther,TypeOther,Wavelength476.0,WavelengthUnitnm},{IDLightSource:0:3,LaserMediumOther,TypeOther,Wavelength488.0,WavelengthUnitnm},{IDLightSource:0:4,LaserMediumOther,TypeOther,Wavelength496.0,WavelengthUnitnm},{IDLightSource:0:5,LaserMediumOther,TypeOther,Wavelength514.0,WavelengthUnitnm},{IDLightSource:0:6,LaserMediumOther,TypeOther,Wavelength561.0,WavelengthUnitnm},{IDLightSource:0:7,LaserMediumOther,TypeOther,Wavelength633.0,WavelengthUnitnm}}

Construct the a list of applied laser wavelengths:

In[12]:=

laserWavelength=Quantity@@@Replace[{"Wavelength","WavelengthUnit"},laserRules,{1}]

Out[12]=

{

405.0

458.0

476.0

488.0

496.0

514.0

561.0

633.0

}

External Links

BioFormatsLink

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Contributed by: Wolfram Staff

Microscope-Specific File Formats

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