Nika: software for two-dimensional data reduction

Abstract

Nika is an Igor Pro-based package for correction, calibration and reduction of two-dimensional area-detector data into one-dimensional data ('lineouts'). It is free (although the user needs a paid license for Igor Pro), open source and highly flexible. While typically used for small-angle X-ray scattering (SAXS) data, it can also be used for grazing-incidence SAXS data, wide-angle diffraction data and even small-angle neutron scattering data. It has been widely available to the user community since about 2005, and it is currently used at the SAXS instruments of selected large-scale facilities as their main data reduction package. It is, however, also suitable for desktop instruments when the manufacturer's software is not available or appropriate. Since it is distributed as source code, it can be scrutinized, verified and modified by users to suit their needs.

Everything SAXS: small-angle scattering pattern collection and correction

“…For some reason, quite a few detector manufacturers worldwide prefer their own image data formats over more standard image formats (a list of some of these formats can be found in the documentation accompanying the NIKA package [80]). This tendency hinders data preservation efforts (though one should preserve corrected and reduced data rather than the original data, a point discussed in section 3.6) and sometimes causes read-in issues of the data in data reduction packages.…”

“…In reality, however, the user can be left to their own devices and an idea on the required steps and sequence may be of some help. Several data processing packages are available to aid the user with the most pressing data correction steps [13,80,95,93] (not an exhaustive list).…”

Neurofilament sidearms modulate parallel and crossed-filament orientations inducing nematic to isotropic and re-entrant birefringent hydrogels

“…SAXS experiments were conducted on the equilibrated hydrogel samples (in the same quartz capillaries) at the Stanford Synchrotron Radiation Laboratory (SSRL BL4-2), acquired on a MarCCD 165 (Fiber Optic-Taper coupled CCD) detector. Scattering data were collected using X-rays with wavelength 1.3776 Å and a sample-to-detector distance of E3.5 m. The unoriented data was integrated over 360°using 'Nika' for Igor Pro 44 to yield the scattering profile. Test samples determined optimal exposure time, and the experimental samples were run for half the exposure time where radiation damage was first observed.…”

NIST Standard Reference Material 3600: Absolute Intensity Calibration Standard for Small-Angle X-ray Scattering

“…The two instrument geometry configurations were calibrated (in Q) using silver behenate (AgBeh). Normalized empty beam scattering runs were used to subtract out parasitic scattering effects, and the two-dimensional SAXS data were reduced using the Nika Igor Pro (Ilavsky, 2012) analysis package.…”