A list of all relevant changes to build 12.0 of the JWST Operations Pipeline is provided in this article. 

Build 12.0 was released as a build candidate in July 2025, and installed as an operations build in August 2025. The information provided here focuses mainly on updates to the JWST Science Calibration Pipeline and associated reference files, but includes information relevant to changes in other subsystems that might affect what users see in their data.

Major updates

Data affected by this build

Provided below is a list of science data products in MAST generated by the JWST Science Calibration Pipeline that may be most significantly affected by the updates in build 12.0. The changes listed in the release notes below may affect other modes as well, but many of these will be transparent to the MAST user.

The data and pipeline stages most affected include:

• Stage 1 processing: Minor updates for nearly all modes.
• Stage 2 processing: significant changes for MIRI imaging, NIRCam/NIRISS WFSS, all spectral TSO modes (MIRI LRS slitless, NIRSpec BOTS, NIRISS SOSS).
• Stage 3 processing: significant changes for all TSO observations, NIRCam/NIRISS WFSS.

Release notes

Build 12.0 of the JWST Operations Pipeline was released as a candidate build on July 17, 2025 and installed as an operations build (12.0) for the Barbara A. Mikulski Archive for Space Telescopes (MAST) on August 26, 2025. The build includes changes to the JWST Science Calibration Pipeline released in version 1.19.1 (of the jwst calibration pipeline package via the PyPI repository. This release also includes changes to the JWST Science Data Processing subsystem (SDP) version JWSTDP-2025.3.1 which is the DMS subsystem that creates raw (uncal) products used as input to the calibration pipeline.

General changes

• Remove the deprecated "Step.__call__" method.
• Read only metadata, not whole datamodel, when getting CRDS references.
• Remove unused cube_skymatch step.
• Code style updates completed for all modules.

Pipeline modules

• In calwebb_spec3 for WFSS modes, reorganize extract_1d output such that a single table extension holds the spectra from all the sources for a given exposure and spectral order. The output datamodel type is now "WFSSMultiSpecModel" instead of "MultiSpecModel". For combine_1d, a single table extension holds the spectra from all the sources, with different extensions representing different spectral orders. The output datamodel type is now "WFSSMultiCombinedSpecModel".
• In calwebb_tso3, reorganize extract_1d multi-integration spectra into a single table, in which each row is a 1-D spectrum. The datamodel for TSO "x1dints" files is now "TSOMultiSpecModel" instead of "MultiSpecModel".
• In calwebb_ami3, revert change to strictness of zip function linking science exposures to PSF exposures, to allow successful processing of associations with differing numbers of science and PSF members.

Product associations

• For nodded NIRSpec FS or MOS spec2 associations, exclude background candidates that do not match the science target ID. For NIRSpec FS spec3 associations, update the product name to include the target ID.

Datamodels

• Add S_REGION keyword to WFSS spectral metadata schema.
• Add new informational processing status keywords to slit and spectral datamodels for NIRSpec multi-slit data.
• Update NIRSpec transforms to support slit name propagation. Add inverse transforms for "Slit2Msa" and "Gwa2Slit".
• Add flat file format for WFSS multi-source "x1d" and "c1d" products.
• Add new spectral models for TSO spectral data, intended to combine all integrations into a single flat table rather than multiple FITS extensions.
• Add a new data array in the regions attribute to IFUImageModel, to hold a pixel-to-slice map for NIRSpec IFU data.
• Add new datamodel "SossBkgModel" to support background reference files for NIRISS SOSS data.
• Change background alias to "bkg_subtract" to fix conflicting aliases for the step. The new alias is the one currently used for running the step or changing parameters from the stage2 pipeline.
• Vectorize "NIRCAMBackwardGrismDispersion" transform.
• Drop support for memory mapping when opening datamodels.
• Deprecate "DataModel.get_fits_wcs" and "DataModel.set_fits_wcs".
• Deprecate dqflags.interpret_bit_flags in favor of astropy.nddata.bitmask.interpret_bit_flags.

Step Changelist

Changes to specific steps in the pipelines are listed below. 

ami_analyze / ami_average step

• Deprecate unused and out of date AmiAverageStep.
• Improve memory usage of AmiAnalyzeStep: for test dataset with 400 integrations and default parameter settings, the memory usage is reduced from 12 GB to 0.5 GB. (Note the scaling is not necessarily linear with the number of integrations.)

• Move pointing information in "AmiOIModel" from "model.meta.ami" to "model.meta.guidestar" (FITS headers remain identical)

assign_wcs step

• Expanded the hard-coded NIRSpec wavelength range to safer limits.
• Populate the wavelength array for MIRI LRS fixed slit data, for consistency with the MIRI LRS slitless mode.
• Rework the NIRSpec WCS to propagate the slit name through all transforms for all modes.
• Attach a pixel-to-slice map to NIRSpec IFU images, in a regions attribute. Optionally (but on by default), use the slice map to revise the WCS to be fully coordinate-based, so it does not require the slice number on input nor report it on output.
• Remove "util.reproject" function (deprecated since 1.18.0). Use stcal.alignment.util.reproject instead.

background step

• Step can now be run standalone with asn or FITS files, given an association with science member containing WCS information from assign_wcs step.
• Fix a bug where highly-masked input data for WFSS modes were raising errors instead of skipping.
• Implement background subtraction for NIRISS SOSS data, fitting reference background templates to background regions of the science data.
• Change background alias to "bkg_subtract" to fix conflicting aliases for the step. The new alias is the one currently used for running the step or changing parameters from the stage2 pipelines.

bar_shadow step

• For NIRSpec multislit data, add a metadata keyword to each slit to record whether it has been barshadow corrected.

clean_flicker_noise step

• Use higher precision for sigma clipping statistics for better numerical consistency across build environments.

combine_1d step

• For WFSS modes, reorganize output such that a single table extension holds the spectra from all the sources, with different extensions representing different spectral orders. The output datamodel type is now "WFSSMultiCombinedSpecModel" for those modes.
• Allow spectra from "TSOMultiSpecModel" to be combined.

dark_current step

• Remove mention and use of dark error array; document extrapolation of darks when science array has more frames than the dark.

emicorr step

• Change the default fitting algorithm for MIRI EMI correction to the "joint" method to improve performance for low numbers of groups.

extract_1d step

• For WFSS modes, reorganize output such that a single table extension holds the spectra from all the sources for a given exposure and spectral order. The output datamodel type is now "WFSSMultiSpecModel" for these modes.
• Reorganize multi-integration spectra into a single table, in which each row is a 1-D spectrum. The datamodel for TSO "x1dints" files is now "TSOMultiSpecModel" instead of "MultiSpecModel".
• Fix crashes in the SOSS ATOCA algorithm when adaptive refinement reaches max grid size.

flatfield step

• Fixed error and variance propagation for inverse steps.
• Set pixels with negative flat fields to NaN and flag as them DNU for NIRSpec data.

fringe step

• Apply fringe correction to VAR_POISSON, VAR_RNOISE, and VAR_FLAT also.

msaflagopen step

• Removed confusing log and warning messages in msa_flagging.

pathloss step

• For NIRSpec multislit data, add a metadata keyword to each slit to record the pathloss correction type applied (POINT or UNIFORM).

photom step

• Apply MRS IFU time-dependent correction to VAR_POISSON, VAR_RNOISE, and VAR_FLAT also.
• Fixed error and variance propagation for inverse steps.
• Update handling for NIRISS SOSS to expect multi-integration spectra in "TSOMultiSpecModel" datamodels.
• Allow NIRCam imaging to match calibration values by subarray, if the photom reference file contains subarray information.

resample step

• Updated documentation to reflect correct definition of pixel_scale_ratio for imaging data: ratio of output to input pixel scales.

• Add options to disable computation of context and variance arrays.

• Removed make_output_wcs, build_driz_weight, and decode_context functions (deprecated since 1.18.0). Use resampled_wcs_from_models, stcal.resample.utils.build_driz_weight, and drizzle.utils.decode_context instead.

saturation step

• Account for non-zero bias in group 2 saturation flagging in frame-averaged groups.

straylight step

• Added option to save shower model when running straylight with clean_showers turned on.

tso_photometry step

• Add support for processing data in units of DN/s by using the gain reference file to convert to flat-fielded electrons.

tweakreg step

• Update docs to clarify format of tweakreg catalogs.
• Make segmentation algorithm respect kernel_fwhm parameter.

wavecorr step

• For NIRSpec multislit data, add a metadata keyword to each slit to record whether it has been wavelength corrected.

white_light step

• Update handling to expect multi-integration spectra in "TSOMultiSpecModel" datamodels. Separate fluxes from different detectors into different output columns.
• Update output table to show correct timestamps and spectral orders for NIRISS tsgrism observations.
• Add BJD_TDB times to output table.
• Fix a crash caused by repeated time stamps in the spectral table. If found, warn and keep only the first one.

JWST Science Data Processing subsystem changes

• TSO files are now evenly segmented, to the extent possible (previously, the final segment was often smaller than the rest).
• A fix was made for a bug introduced in Build 11.3 that stopped creating previews for "_x1dints.fits" files. On the other hand, previews are now no longer made for any WFSS data.
• Added new calibration keyword BKGD_SCL (background scale factor) to the Background information section of the primary FITS header for FITS files at level-2b and above.