EMUE-D5-1-PixelVoxelUncertainty

This example illustrates the effect of considering a 2D or 3D image as a set of pixels or voxels on a computed quantity: computed tomography application and nanoparticle sizing by AFM.

The files of this dataset comprise supporting information to the example EMUE-D5-1-PixelVoxelUncertainty of uncertainty evaluation of the compendium made by the EMUE consortium (Euramet EMPIR project EMUE).

It is also related to example EMUE-D2-4-NanoparticleHeightMeasurements, also present on Zenodo.

The LaTeX source of the document is also attached to the document.

Please contact the authors for any question you might have about the following content and its possible use.

• CT_scan_tumour_mass_voxel_coordinates.csv: data listing of pixel coordinates (X, Y) for the example of tumour imaging. The properties computed in the example all use the m=38 data, but m=56 data are also provided.
• NP_AFM_model_2D.csv: 2-dimensional model of the PDF of the pixel-size uncertainty computed for nanoparticle sizing. Only the continuous part of the distribution is present (that is, the Dirac delta part of the distribution is to be added by the user when using the file). The values are tabulated as r/X ("rX"), h/(2r) ("Hr2") and the density probability computed by the model ("PDF").
• RM8012_s20170720_*_*.png: Images of the processed measurement images of nanoparticles by AFM, with nanoparticles identified. The color of the label refers to the measured height for the nanoparticle, with color scale given on the right, common to all pictures. The last number in the file name is the resolution (number of pixels in each of the x-y directions).
• NP_AFM_animation_aligned.gif: Animation of measurement images of nanoparticles by AFM , from coarser pixel size to finer one. Measurement images have been shifted, correcting for the instrument drift from one image to the next one. The nanoparticle labels have their color associated to the measured nanoparticle height, according to the color Z-scale given on the right. Smaller measured size is observed for coarser pixel size.
• NP_AFM_meas_data.Rdata: R data file with nanoparticle data, and matching across images.
• * vSheetRef: is the vector of tags used for the images. They refer to the respective resolutions, appended with _2 for resolution which have two images at the same resolutions.
• * vPixRef : is the vector of the resolution of the images.
• * vIdRef: is the vector of the identifiers (IDs) of the same nanoparticle that could be identified on all the images, and which is considered as reference to perform the matching (alignment) of the different images.
• * rawData: is a named list (named according to the tags in vSheetRef) of the measured data of all of the nanoparticles. Each line corresponds to a nanoparticle, with its unique identifier "ID" in the image at hand. For nanoparticle sizing, the "Z Maximum" is the measurand.
• `X Center of Gravity, Material` and `Y Center of Gravity, Material`: are the reconstructed nanoparticle positions on the X and Y axes, respectively. Other observables are also made available but not used for the current purpose.
• * v_full_matched: matchings which are agreed upon from all the pixel size images, unanimously. Each line is a set of identifiers "ID" of the same NP, but as measured on all the images, each column corresponds to an image (with column name being the tag, as appearing in vSheetRef).
• vPixRef, vSheetRef, vIdRef are commonly ordered along the images.