The STIS CCD is a 1024 X 1024 pixel, thinned, backside illuminated SITe CCD, with sensitivity from below 2000 Å up to about 11000 Å. In a space environment, CCD detectors accumulate radiation damage, which over time leads to increasing dark current, more hot pixels, and reduced charge transfer efficiency. After fifteen years on orbit, the effects of such radiation damage on the STIS CCD have become substantial.
The Charge Transfer Efficiency (CTE) measures the fraction of the charge in a given pixel that is transferred to the next row during the readout. The CTE is in practice always less than unity because some of the charge is caught in "Traps" in the pixel and is left behind during transfer of that pixel to the readout amplifier. The fraction of charge lost depends on the signal levels of both the source and the background. Losses are most substantial for faint sources on low background levels. Since in a CCD, charge must be transferred many times before reaching the readout register, even a small decrease in CTE can have a large effect on the measured count rate near the center of the detector. For n transfers, the fraction of detected charge will be CTEn. The measured Charge Transfer Inefficiency (CTI=1 - CTE) of STIS has steadily increased over the years. For very faint sources near the center of the detector, a substantial fraction of the counts collected by the detector can easily be lost during the readout.
Most of the charge lost during a transfer will reappear during a later transfer. This leads to the appearance of "charge tails" below the sources. These trails impact photometry, noise, and astrometry of sources. CTI trails remove flux from the central pixel and thus degrade the expected S/N for an observation (for example, see Figure 4 of ISR 2011-02). CTI trails bias centroid measurements of sources along the trail direction, which can severely impact high precision astrometry. Finally, trails from warm pixels and cosmic rays introduce noise in an observation and increase the noise within calibration files such as routine darks.
The best way to ameliorate these problems is to move the source closer to the readout of the detector, especially for spectroscopy. To this end, a number of years ago, new "E1" aperture positions were defined in the long STIS slits to place the target near row 900 of the CCD, much closer to the readout register. This reduces the number of transfers during the readout by about a factor of four. In addition to reducing CTI losses, placing the source spectrum closer to the readout register substantially reduces contamination by the CTE "Tails" of cosmic rays and hot pixels. Also, the dark current is noticeably lower near the top of the detector.
While the CALSTIS software does include an algorithm to correct the extracted flux of a point source spectrum for CTE effects, it cannot restore the lost signal-to-noise and is not applied to imaging. Use of the E1 aperture positions is strongly recommended for all but the very brightest or most extended spectroscopic point sources. Note also that, while the STIS Spectroscopic Exposure Time Calculator does not currently include correction for CTE effects, the effects can be estimated using an iraf script available at http://www.stsci.edu/hst/stis/software/analyzing/scripts/cteloss_descrip.html
Additional information about the STIS CCD CTE and the algorithm for correcting the fluxes of point-source spectra can be found in Goudfrooij et al. (2006 PASP, 118, 1455).