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 version 1.12.5, the default source finding algorithm is 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). There are plans to update the default algorithm to IRAFStarFinder in future pipeline versions. In the interim, users can improve the image combination of NIRISS images by creating custom source catalogs (e.g., using IRAFStarFinder) and use those in the tweakreg step using the use_custom_catalogs parameter.
  • 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.


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

Originally published