NIRISS Imaging Known Issues

Known issues specific to NIRISS imaging data processing in the JWST Science Calibration Pipeline are described in this article. This is not intended as a how-to guide or as full documentation of individual pipeline steps, but rather to give a scientist-level overview of issues that users should be aware of for their science. 

On this page

Specific artifacts are described in the Artifacts section below. Guidance on using the pipeline data products is provided in the Pipeline Notes section along with a summary of some common issues and workarounds in the summary section.

Please also refer to NIRISS Imaging Calibration Status for an overview of the current astrometric, photometric, and target acquisition accuracy of NIRISS Imaging data products.


Information on NIRISS instrument artifacts are found on the main NIRISS Known Issues page.

Pipeline notes


In calwebb_image2 stage, the world coordinate system (WCS) is assigned, the data are flat fielded, and a photometric calibration is applied to convert from units of count rate (ADU/s) to surface brightness (MJy/sr).

By default, the background subtraction step and the resampling step are turned off for NIRISS imaging at this stage of the pipeline.


In calwebb_image3, the individual calibrated files (*_cal.fits) for each of the dither positions are combined to one single distortion corrected image. An association file needs to be created to inform the pipeline that these individual exposures are to be combined together.

By default, this stage of the pipeline performs the following steps on NIRISS data:

  • tweakreg - creates source catalogs of point-like sources for each input image. The source catalog for each input image is compared to each other to derive coordinate transforms to align the images relative to each other.
    • As of CRDS context jwst_1156.pmap and later, the "pars-tweakreg" parameter reference file for NIRISS performs an absolute astrometric correction to GAIA data release 3 by default (i.e., the abs_refcat parameter is set to GAIADR3). Though this default correction generally improves results compared with not doing this alignment, it can sometimes result in poor performance in crowded or sparse fields, so users are encouraged to check astrometric accuracy and revisit this step if necessary.
    • As of pipeline build 10.2 and CRDS context jwst_1223.pmap and later, the "pars-tweakreg" parameter reference file for NIRISS uses IRAFStarFinder as the default source finding algorithm. This algorithm improves on the performance from the previous default option (DAOStarFinder) which can result in up to 0.5 pix uncertainties in the centroids for undersampled PSFs, like the NIRISS PSFs at short wavelengths (Goudfrooij 2022)
  • skymatch - measures the background level from the sky to use as input into the subsequent outlier detection and resample steps.
  • outlier detection - flags any remaining cosmic rays, bad pixels, or other artifacts not already flagged during the calwebb_detector1 stage of the pipeline, using all input images to create a median image so that outliers in individual images can be identified.
  • resample - resamples each input image based on its WCS and distortion information and creates a single undistorted image.
  • source catalog - creates a catalog of detected sources along with measured photometries and morphologies (i.e., point-like vs extended).
    • Useful for quicklooks, but optimization is likely needed for specific science cases.

Summary of common issues and workarounds

The sections above provide detail on each of the known issues affecting NIRISS imaging data; the table below summarizes some of the most likely issues users may encounter along with any workarounds if available. Note that greyed-out issues have been retired, and are fixed as of the indicated pipeline build.

SymptomsCauseWorkaroundFix buildMitigation Plan

NR-I01: When the peak pixel of a star (or other compact object) reaches beyond ~25,000 ADU in an integration (after bias and dark subtraction and linearity correction), it starts "spilling" charge to its neighboring pixels. This causes an effective "widening" of the PSF or charge distribution, as well as flux loss for those objects in the combined, resampled products of the calwebb_image3 stage of the Science Calibration Pipeline. This effect is strongest for the most undersampled modes (i.e., filters with pivot wavelength <= 2 μm).

This is due to the so-called "brighter-fatter effect" (BFE) that affects near-IR H2RG detectors, in combination with the current way "jumps" are detected and dealt with in the calwebb_detector1 pipeline stage, and how the latter affects image combination in the calwebb_image3 pipeline stage.

No efficient workaround is available at present.

Updated Operations Pipeline

Apply a new Science Calibration Pipeline step called charge_migration within the calwebb_detector1 stage (Goudfrooij et al. 2024). STScI is reprocessing affected data products with an updated Operations pipeline, installed on December 5, 2023.  Reprocessing of affected data typically takes 2–4 weeks after the update.

NR-I02: WCS keywords in the header of pure parallel imaging observations taken prior to June 12, 2024, are "off" by of order 0.1 arcsec no matter which SI is prime, and the offset is generally different for different dither positions.

In JWST data, the header keywords that are used to determine precise WCS information use the guide star coordinates. In pure parallel data taken prior to June 12, 2024, these coordinates were unknown prior to execution. This is why for those pure parallel data, the WCS were determined by using a "coarse" algorithm, leading to the accuracy issue.For the data affected by this issue, a Python script has been made available in this GitHub repository to correct the relevant WCS header keywords in the products of the calwebb_detector1 pipeline, i.e., the “_rate.fits” and/or “_rateints.fits” files. After that script has been run on the input file(s), one can then (re-)run stage 2 of the JWST pipeline (calwebb_image2 and/or calwebb_spec2) on those files, which will then have correct WCS header information.

10.2 (for data taken after June 12, 2024)

Updated Operations Pipeline

This issue was fixed in JWST operations as part of build 10.2 of the JWST Science Calibration Pipeline (June 12, 2024). Data taken after that date do not have this issue anymore.


Goudfrooij, P. et al. 2024, PASP, 136, 4503
An Algorithm to Mitigate Charge Migration Effects in Data from the Near Infrared Imager and Slitless Spectrograph on the James Webb Space Telescope

Goudfrooij, P. 2022, JWST-STScI-008116
Accuracy and Precision of Centroid Algorithms in the photutils Python package for NIRISS Point Spread Functions

Notable updates

    Updated issue NR-I02 to note that the default source finding algorithm in tweakreg for NIRISS (specified by the pars-tweakreg parameter reference file) is IRAFStarFinder as of pipeline build 10.2 and CRDS context jwst_1223.pmap.

    Added issue NR-I02: WCS keywords in the header of pure parallel imaging observations are "off" by about 0.1 arcsec

Originally published