NIRSpec Instrument Features and Caveats

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The JWST NIRSpec instrument has a number of features and characteristics that observers should be aware of when planning observations and interpreting data. This article provides an overview of several areas about which users should be aware.

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Detector considerations

1/f noise

JWST's near-infrared HgCdTe detectors have a correlated noise, known as 1/f noise, that is introduced by the detector readout system (Moseley et al. 2010). This noise results in horizontal striping, as illustrated in Figure 1. With NIRSpec's IRS2 readout mode, reference pixels are interspersed with the sampling of normal pixels to mitigate the 1/f noise. However, this noise will still be present in data taken with NIRSpec's traditional detector readout mode; this includes all observations made with NIRSpec's subarrays, where IRS2 is unavailable. In these cases, it may be necessary to use background pixels in the horizontal bands to estimate and subtract the 1/f noise.   

Figure 1. High temporal correlation (1/f noise) seen as striping in the horizontal direction

The high temporal correlation (1/f noise) is seen as striping in the horizontal direction in this smoothed exposure acquired with the traditional readout mode. (The vertical flux offsets are due to different bias levels in the four detector outputs).


The detectors used in JWST's near infrared instruments (NIRCam, NIRISS, and NIRSpec) all experience large cosmic ray events known as snowballs. Pipeline algorithms to address these artifacts are under development; in the interim the best mitigation strategy is to dither. 

MSA characteristics

NIRSpec's micro-shutter assembly (MSA) allows, for the first time, slit-based multi-object spectroscopy (MOS) from space. Nonetheless, the MSA has a number of characteristics that impact data taken in both MOS and IFU mode. It is important to understand these characteristics and how they may impact data.

MSA leakage

See also NIRSpec MSA Leakage Correction for IFU Observations, NIRSpec Bright Spoilers and the IFU Recommended Strategies,  NIRSpec MSA Leakage Subtraction Recommended Strategies.

The contrast achieved by the MSA is finite since light from sufficiently bright sources can leak through the MSA to cause an imprinted signal on both MOS and IFU observations. A characterization of this leakage is given in NIRSpec MSA Leakage Correction for IFU Observations, and mitigation strategies are discussed in NIRSpec Bright Spoilers and NIRSpec MSA Leakage Subtraction Recommended Strategies.

MSA leakage could be especially problematic when taking NIRSpec IFU observations of nearby galaxies or star-forming regions, where the closed MSA is illuminated by a large, yet spatially variable, astronomical object. In any cases where leakage is determined to be a significant source of contamination, and cannot be removed by dithers or nods, it may be advantageous to take one or more exposures with the MSA commanded closed (known as "leakcals").  

At this time, we are still gaining experience with MSA leakage in real observations. Users should expect that our understanding of it may evolve from pre-launch models (Deshpande et al. 2018), but at the time of the Cycle 3 Call for proposals, updated information is not available. Therefore, it is recommended that observers concerned with MSA leakage plan conservatively, and consult the JWST Help Desk as needed. 

MSA operability

See also NIRSpec Micro-Shutter Assembly, NIRSpec MSA Shutter Operability

A fraction of the MSA shutters are failed closed and a handful are failed open. A detailed discussion of this MSA characteristic can be found in NIRSpec MSA Shutter Operability. While the MSA Planning Tool (MPT) has been designed to plan around these shutters, it is important to understand that the MOS operability evolves with time. Relative to ground tests, the fraction of failed closed shutters has increased slightly since launch. The MOS operability was monitored during Cycle 1 to determine if it is stable in space. Updates to the operability map are provided as necessary, and will be accessed by  Astronomer's Proposal Tool (APT) whenever the tool is restarted (provided an internet connection is available). Hence, MOS users may wish to double check their final flight-ready configurations close to their submission deadline. The article NIRSpec MSA Shutter Operability provides instructions for checking whether a previously planned configuration is negatively impacted by a new failed shutter. This same article gives advice on resolving the conflicts between previously planned sources and new failed shutters.

Unidentified optical shorts

One known characteristic of the MSA is that electrical shorts can occur at a particular shutter location. There is a procedure in place that identifies these shorts using telemetry of electrical currents and masks them in order to prevent the possibility of damage to the array. However, some shorts are too weak to be readily identified via elevated current, but rather manifest themselves by producing a glow caused by heating of the area around the shutter. These "optical" shorts are identified using dark exposures and subsequently masked. Nonetheless, there is a  possibility that some may appear between calibration checks during normal operations, which could then contaminate science data. This would manifest in dispersed data as a spectrum with roughly a blackbody shape. Users should check for any unexpected dispersed signal in their images not related to the already-known failed open shutters (which are flagged in the DQ array of the level 2b data products). Nod subtraction may remove the signal, but in some cases a repeat of the observation may be warranted. Observers wishing to request a repeat should file a Webb Operations Problem Report (WOPR).

MOS wavelength coverage

See also NIRSpec MOS Wavelength Ranges and GapsMSA Target Info File

The wavelength coverage achieved for a given object will depend on its position in the focal plane. For example, sources further to the right in the projected NIRSpec field of view will also have their spectra projected further to the right on the detector, as shown in Figure 2. With all of NIRSpec's dispersers, it is possible for some wavelengths to fall in the gap between NIRSpec's 2 detectors, and in the high-resolution gratings, some wavelengths can fall off the edge of the detector. Further details are provided in NIRSpec MOS Wavelength Ranges and Gaps. Users interested in precise wavelength coverage for sources in a MOS observation can find them by exporting the MSA target info file.

Figure 2. A View of NIRSpec MSA Data

An example of NIRSpec MOS mode spectra taken with a calibration flat field lamp, providing uniform illumination, and an MSA shutter slitlet configuration using the G140M+F100LP spectral configuration. Two examples of the planned MSA spectral slitlets are highlighted in the upper left. The fixed slits are always open and, therefore, always appear in MSA science mode exposures. Pointers also show zero-order images of the right spectral slitlets—these zero-order slit images are seen in the medium resolution (R ~ 1,000) spectral configurations and appear on detector NRS1. These images are associated with spectra on (approximately) the same row on the right side of the NIRSpec data on detector NRS2 (see pointers in yellow). The failed open MSA shutters appear as single shutter spectra (examples are highlighted at right). The gap between the NIRSpec detectors is not shown to scale.

NIRSpec calibration plan

Instrument model-based calibration

The NIRSpec calibration plan, including flux and WCS (wavelength in vacuum) calibrations, makes use of a parametric model of the optics and components of the instrument as its backbone (e.g., Dorner et al. 2016). This instrument model is itself calibrated using an extensive set of internal lamp exposures in all observing modes, plus imaging observations of the astrometric calibration field. The instrument throughput is then calibrated using a combination of internal lamp exposures and observations of spectrophotometric standard stars.

There are 2 key aspects of the calibration of interest to users:

  1. The grating wheel assembly (GWA) exhibits some repositional inaccuracy; any time it is moved, it does not return to the exact same position for a given setting. This causes shifts in the position of spectra on the detector in the dispersion direction, of up to several pixels. However, NIRSpec was designed with sensors on the GWA that report its position each time it is moved. A key part of the instrument model is a calibration of the sensor voltage as a function of the grating tilt. The GWA tilt calibration is then used in combination with the model and sensor telemetry to calculate the instantaneous wavelength solution per pixel on the detectors for each and every exposure. This calibration strategy is expected to yield a wavelength solution that is good to better than 1/8th of a resolution element for all dispersers.

  2. NIRspec's flat fields are broken into 3 components that separate different parts of the instrument throughput (Rawle et al. 2016). Pixel-to-pixel quantum efficiency variations in the detectors are handled in the "D-Flat." The throughput of the spectrograph optics and dispersers is corrected by the "S-flat" (calibrated using internal flat lamps), while the throughput of the Optical Telescope Element (OTE) plus fore optics and filter wheel is treated by the "F-flat" (calibrated using spectrophotometric standard stars). These last 2 components include both spatial and wavelength dependencies. Of particular interest, the "S-Flat" for MOS is complicated by the fact that different shutters project the same wavelength onto different detector pixels. Because it is impractical to obtain dispersed lamp data through all quarter-million shutters, we instead observe a smaller sample of long slits (opening one entire column of shutters at a time) spaced across the MSA. The S-Flat correction for a specific shutter and wavelength is then interpolated from these measurements. The accuracy is set by the S/N of each lamp exposure and the interpolation uncertainty.

Ground testing indicated that this approach would meet NIRSpec's science requirements. The overall accuracy in the wavelength and throughput characterization is sufficient for most science use cases, obviating the need for dedicated flat field and wavelength calibration exposures (i.e., "autocals") with every science exposure. However, for observations requiring very high flux or wavelength precision, users should contact the JWST Help Desk for further guidance.

Post-launch FFLT and SFLT reference files are available for use with the calwebb_spec2 pipeline. These reference files were determined in a hybrid manner, comprised of the predicted pre-launch throughput of the optical telescope element (OTE) combined with the NIRSpec instrument model derived from analysis of commissioning data. Ongoing analysis of the commissioning and Cycle 1 data will lead to flat field reference files that are wholly consistent with post-launch data, and they will be incorporated into a future version of the pipeline. The hybrid approach does not account for the significant improvement in throughput indicated by in-flight data. Analysis of the NIRSpec commissioning observations has shown that the overall wavelength dependent instrument efficiency can differ by up to 40% (Boeker et al. 2022, Giardino et al. 2022).

In general, new reference files will be incorporated in the operational pipeline and will automatically be used to calibrate new data. Previously ingested data in MAST will be reprocessed with the new reference files over a period of several weeks after a new build release date. Users can also opt to manually reprocess the level 2a data products with the latest CRDS context map (see the "Context History" table in the JWST Calibration Reference Data System (CRDS) page). 

Absolute flux calibration

See also JWST Data Absolute Flux Calibration

The calibration of the "F-flat" throughput component and the conversion to physical flux units is done using observations of spectrophotometric standard stars. A limited number of stars were observed during commissioning. Consequently, systematic uncertainties introduced by differences in the stellar models dominate the absolute flux calibration accuracy in Cycle 1. A larger sample of stars of different types is being observed with all modes (and multiple instruments, allowing cross-calibration) over the course of Cycle 1 and future cycles, thereby reducing systematic uncertainties.  It is expected that the absolute flux calibration will reach significantly better than the 10% accuracy requirement.  A detailed discussion of JWST's flux calibration plan can be found in Gordon et al. (2022).


Böker, T., Abul-Huda, Y., Altenburg, M. et al., 2022, arXiv:2208.02860
In-orbit Commissioning of the Near-Infrared Spectrograph on the James Webb Space Telescope

Deshpande, A., et al. 2018, SPIE Proceedings Vol. 10698
The contrast performance of the NIRSpec micro shutters and its impact on NIRSpec integral field observations

Dorner, B., et al. 2016, A&A, 592, 113
A model-based approach to the spatial and spectral calibration of NIRSpec onboard JWST

Giardino, G., Bhatawdekar, R., Birkmann, S. M. et al., 2022, arXiv:2208.04876
Optical throughput and sensitivity of the JWST NIRSpec

Gordon, K.D., et al. 2022, AJ, 163, 267
The James Webb Space Telescope Absolute Flux Calibration.  I.  Program Design and Calibrator Stars

Moseley, S. H., et al. 2010 SPIE Proceedings Vol.  7742
Reducing the read noise of H2RG detector arrays: eliminating correlated noise with efficient use of reference signals

Rawle, T. D., et al. 2016,  SPIE Proceedings Vol. 9904
Flat-fielding strategy for the JWST/NIRSpec multi-object spectrograph

Latest updates

  • Added note about repeating observations impacted by MSA shorts.

  • Added availability of new flat field reference files.
Originally published