Marc Kassis, Robert Kibrick, Connie Rockosi, Gregory D. Wirth



In May and June 2009, WMKO and UCO/Lick installed and commissionined a new red-side dewar for LRIS featuring a new detector mosaic. This long-awaited upgrade to the instrument offers numerous benefits to LRIS observers: Along with the new detector, several other changes to LRIS affect the way observers will use the upgraded instrument. This document describes the various changes and their implications for observing.

Red Dewar Characteristics

Physical Description

The new LRIS-R mosaic consists of two 2k×4k LBNL high-resistivity CCDs. These devices offer significantly higher quantum efficiency (QE) in the red that significantly extends the usable wavelength range of the red side of LRIS, extending coverage into the I band. Plots of the QE curves for each device in the mosaic are attached later in this document. In addition, images taken with these CCDs do not suffer from interference fringes, thus reducing the impact of instrumental flexure on flat field corrections.

In addition, these CCDs provide a larger detector area, smaller pixels (15 μm versus 24 μm in the Tektronix/SITE 2k×2k CCD), and a flatter focal plane. Because the area per pixel is now 40% of what it used to be, observers may want to bin pixels during CCD readout, and both row and column binning are supported.

Unlike the Tektronix/SITE 2k×2k monolithic CCD they replace, the CCDs in the LRIS-R mosaic are not production science-grade devices from a commercial vendor. Rather, they are early prototype devices from LBNL, and as such, they have more traps, cosmetic defects, and other anomalies than in typical science-grade devices. These foibles are described in the accompanying section on cosmetics.

Detector Characteristics

Quantum Efficiency

The quantum efficiency curves as measured in the lab at Lick are presented below. These curves are reproduced from PDR and DDR documentation.

QE for detector 1-12 QE for detector 1-13

Gain & Readnoise

The gain and readnoise of the new mosaic depend on the selected CCD gain and readout speed. Under normal operations, observers will use "normal" CCD speed with the gain set to "high" while binning 1x1, 1x2, 2x1, or 2x2. The following table provides CCD parameters for this operating mode. For gain and readnoise values corresponding to other CCD speed and gain settings, please see the separate report on red-side gain and readnoise.

LRIS-R Detector Characteristics
CCDSPEED=normal and CCDGAIN=high
VidInp Amplifier Gain Noise Dark Current
[e-/DN] [DN] [e-] [e-/px/hr]
1 1-12L 1.022±0.005 4.57 4.67 1.7*
2 1-12R 0.955±0.005 3.97 3.79 1.7*
3 1-13L 0.877±0.006 3.39 2.97 1.3*
4 1-13R 0.916±0.005 3.38 3.10 1.3*
*Dark current measurements should be considered preliminary and represent an upper bound. Actual dark current may be slightly lower.

Readout Times

The new red mosaic offers three readout speeds: The following table gives the minimum times required to acquire a full-frame LRIS exposure in various red detector operating modes.

LRIS-R Mosaic Readout Times
CCDSPEED Binning Readout Time*
Normal 1x1 1:44
Normal 1x2 1:05
Normal 2x1 1:10
Normal 2x2 0:49
Fast 1x1 1:09
Fast 1x2 0:48
Fast 2x1 0:53
Fast 2x2 0:41
*Elapsed time for 0 sec exposure, including erase, expose, and readout phases.


In contrast to the old red detector system, the onset of non-linearitry occurs before the saturation of the ADC (65,536 DN). Observers should strive to keep the peak signal level below 50,000 DN to ensure that they are operating in the linear regime.

Pattern Noise





Traps and bad columns


Flatfielding variations

The LRIS-R detectors exhibit some cosmetic features in both CCDs that present a flatfielding challenge. The tape effect is a QE variation seen in the 100 columns of both CCDs adjacent to the gap that results from the effect of packaging the detectors. Additionally, one of the detectors (red CCD2, which is the one aligned with CCD1 of the blue mosaic) was damaged by a handling procedure during manufacture, resulting in large-scale arc- and box-shaped variations in the detector response. These artifacts are readily seen on any raw image.

The ampliture of the tape effect is roughly a 2% variation in the flats, which fortunately flatfields out perfectly at all wavelengths. In the I-band, the chuck-pattern defects have an amplitude of about 1% in the raw data and are undetectable in a flat-fielded frame. In R, the chuck-pattern amplitude is about 3% in the raw data. After flat-fielding, the residual pattern remains with an amplitude of about 1%. Before and after pictures for R and I images appear below.

LRIS-R R-band Image Before and After Flatfielding
R-band image before and after flatfielding
Note artifacts visible in raw image at left; much reduced in flatfielded image at right.

LRIS-R I-band Image Before and After Flatfielding
I-band image before and after flatfielding
Note artifacts visible in raw image at left; much reduced in flatfielded image at right.

Lab tests showed that the QE variations from the chuck pattern were worst at blue wavelengths, so the flatfielding variations on the red mosaic are expected to be even greater in V. It is possible that more work and care with the flats will improve the situation in the R and V paassbands, but observers should be aware of this issue.

The other CCD (1-12, CCDLOC=1) does not suffer the same vacuum-chuck damage during fabrication and so does not show the same features. Although it does exhibit the tape effect, flatfielding appears to remove these artifacts on CCD 1-12 quite effectively.

Note that the bright area visible from about column 15 to 35 (columns < 15 are masked) is yet another kind of image artifact. It is an edge effect that is additive, not multiplicative, and probably has to do with photons collected in the dead area of the CCD outside the imaging area leaking into the first few columns. It is much less pronounced in spectroscopic frames, possibly because there are fewer photons as compared to an imaging frame.

Radiation events

The new CCDs are much better detectors of cosmic ray events than the ones they replaced, which is a nice way of saying that observers can expect to see a higher rate of cosmic ray events in their images than before. The rate of cosmic ray and other radiation events is such that in a 1200 second dark exposure, between 0.7% and 1% of the pixels are contaminated at a level more than 5σ above the background bias. The expected muon rate, taken from work done by the LBL group, Stover and others (e.g., Smith et al. 2002, Proc. SPIE, 4669, 172) in the process of characterizing these fully-depleted, thick CCDs, is about 390 events per quadrant of the mosaic. That suggests an average size for the trails of 100 pixels. The actual distribution of event sizes in pixels is extremely broad, but 100 is reasonably close to the mean. The majority of the tracks are straight, indicating that the shielding is doing its job of keeping out local low-energy electrons. An example of part of a frame is seen below.

Cosmic Rays in an LRIS-R Dark Image
Portion of an LRIS-R dark image showing numerous cosmic
	  ray event

Image Quality

The minimum FWHM at best focus for imaging and longslit mode is comparable to that seen on the blue side. The 100 µm gradient seen in the focus in the spatial direction in the old red side is considerably less steep. A direct comparison will require more work to distinguish changes to the focus software from changes to the data. We will also analyze longslit focus data to check the image quality in the new detector real estate. The bottom line from the analysis so far is that image quality is, at worst, unchanged.


Comparison to Original Red CCD

Steve Allen of UCO/Lick has kindly produced the following diagram comparing the area of the new mosaic (shaded region) to the previous red-side CCD (white outline).

LRIS-R Science Mosaic Geometry
Geometry of the red CCD mosaic


The red and blue LRIS imaging data for this analysis are of the sparse globular cluster Palomar 5 using unpublished astrometry generously shared by Kyle Cudworth. Each of the two quadrants on either side of the gap have about 100 matches to Cudworth's catalog, and the median offset between the astrometric solution computed from a subset of that sample and the entire 100 stars is 0.18 arcsec, with only a few outliers.

Based on these images, the plate scale of the new red mosaic is 0.135 arcsec/pix in both the column and row directions. Using the plate scale for the old CCD of 0.211 arcsec/pix, the scale for the new mosaic should have been changed by the ratio of the pixel sizes, 15/24, to 0.132 arcsec/pixel. The difference is 2.5%.

A plot of the layout of the focal plane on the sky for this image of Pal 5 is seen below. Note that this frame was taken at PA=-90° to get maximum overlap with the Pal 5 astrometric catalog. For a PA of 0°, rotate RA,Dec relative to the pixel coordinates. The red CCD on the north side of the gap in this frame is 1-13 in Lick's nomenclature, and is labeled as such and as CCDLOC=2 in the headers. The red quadrant that borders the gap to the North is HDU 4 in the FITS files, and is labeled as extension (HDU) vidinp4 in the header. The northmost quadrant is HDU3, vidinp3. On the south side of the gap, the red CCD is labeled CCDLOC=1, CCD 1-12 in Lick's nomenclature. The quadrant on the gap is HDU 1 in the FITS files, vidinp1. The other quadrant, furthest south, is vidinp2.

LRIS Red and Blue FOV Projected Onto Sky
On the blue side, CCD1 (as labeled with CCDLOC) is on the north side of the gap. FITS extension HDU 3 (vidinp3) borders the gap, and vidinp4 (HDU 4) is northmost. The blue CCD on the south side of the gap is CCD0, with HDU 2 (vidinp2) next to the gap and vidinp1 (HDU 1) southmost.

On either side of the gap for both the red and blue mosaics, pixel pixel 0,0 (row, column; x,y) of each quadrant is at late RA. Pixel 0,4095 is at early RA.

Again, mapping between pixel and RA,Dec will change for different PAs. This is just to help get oriented between red and blue.

Red/Blue alignment at the gap

The two CCDs on the north (in this image) side of the gap are the lowest-noise red and blue CCDs. Those are hdu4, CCD2 on the red and CCD1, hdu3 on the blue. Column 0 of those two CCDs are offset from one another by 1.8 arcsec at pixel 0,0 (the high RA side in this picture) and 2.7 arcsec at pixel 0,4096 (the low-RA corner). The offset parallel to the gap (which in this frame is almost exactly an offset in RA) is 15.4 arcsec or 111 pixels.


The red CCDs are slightly tilted with respect to one another. The gap, specifically the distance between the first column of the two red CCDs, at pixel (0,4096) is 24.96 arcsec and at pixel (0,0) is 27.91 arcsec.

User Interface

We have made changes to the observing software to accommodate the changes to the GUIs and image display. At the end of the lris startup procedure launched by selecting the appropriate background menu item, the observing software is auto-arranged. During the auto-arranging, DS9 displays are resized so that images are displayed as large as possible. Below are three screen shots of the displays that show the layout of the observing software after auto-arrangement.

Left-most desktop

Left-most desktop

Left-most desktop

Image Display

FIGDISP -> ds9 Image background on ds9 has the same color as the xpose gui

Compass roses

The Red and Blue image displays rotate and flip images such that both the red and blue orientations are the same. Although the compass roses have the same orientation, both the red and blue displays have a compass rose.

There is a known problem with the compass roses. Although the compass roses correctly indicate North on the images, the EW coordinates are flipped (wrong handedness). We plan to fix this problem but currently it is lower priority.

Wavelength Axis

Blackbelt observers have or will notice that the Red and Blue side displays are on opposite screens relative to the displays before teh upgrade. This may seem backwards at first, but the new format has an advantage. On both image displays, the spectral direction is horizontal (L->R) on the display. Also both display have the bluest wavelengths on the left hand side of the display and the redest wavelengths on the right. Thus, observers should see their object spectra increase in wavelength from left to right across both displays.


The advent of the new red mosaic required numerous changes to the LRIS software. Some notable changes affect slitmask alignment and motion scripts.

Slitmask Alignment

The venerable xbox task is history, replaced by lbox. Rather than call this task directly, we recommend that observers make use of the following convenient tasks:
check_boxes (replaces check_boxesb)
Use this script when trying to identify your alignment stars on a direct image of your slitmask field. It will display the selected LRIS image on the ds9 display and mark the corresponding locations of the alignment boxes as shown in your coordinate files. Optionally invokes lbox when done. Supports both red and blue sides.
do_check_boxes(replaces do_check_boxesb)
Use this script when acquiring slitmask alignment images with the mask in place. This script will wait for the image currently in progress to read out, check the slitmask name in the image header, locate the corresponding box file, and launch check_boxes so that you can verify and adjust the box locations as required so lbox can find them. Since it determines the image name and coordinate file automatically, it helps prevent those late-night mistakes that can cost you valuable time. Note: this task can't be used on direct images, since it won't be able to determine the mask name. Supports both red and blue sides.
do_lbox (replaces do_xboxb)
You can use this task instead of do_check_boxes if you are confident that your box locations are secure and thus don't require the visual confirmation offered by check_boxes/do_check_boxes. Skipping the display of the image saves some time, so this method is faster. This script will wait for the current image in progress to read out, then it will run lbox on it (if no image is in progress, it reads the latest image from disk). Can be used with either the red or blue side.

Motion Scripts

Use movr and movb for executing telescope moves on the red and blue sides, respectively. The IRAF tasks mshift and mshiftb no longer exist. The gmov script can be used for motion on the old movable offset guider only; will not work with the new slit-viewing guider due to the different rotation and scale.

Detector Operation

Clock Delay Calibration

The noise measurements tabulated above correspond to the results that can be achieved when the serial clock delay parameter (keyword LSERCLKD) has been optimized for the particular combination of: The support staff will optimize this parameter before observing. When optimized, the gain and noise at a particular readout speed and preamplifier gain setting will be the same regardless of the operating temperature or binning.


Unlike the blue CCD mosaic, the red CCD mosaic may be set to read out any desired rectangular region. Windowing is now accomplished using the PANE keyword. Observers can modify the PANE keyword directly either by updating the keyword via the command line or using the window selection on the Xpose GUI. Windowing the CCD in the spatial direction will not save readout time. Windowing the CCD in the spectral direction will save time, but will reduce wavelength coverage and thus is not typically something the observer wants to do.

On the CMD... menu available on the red Xpose GUI, there are options for windowing the CCD:


Observers should bin the detector in the spatial and/or spectral direction for two reasons: Four commonly used binning modes are available on the CMD... menu available from the Xpose GUI. These modes are 1x1, 1x2, 2x1, and 2x2. Selecting these modes does not change how the CCD is windowed. Note that these scripts will set the CCD readout speed to normal.

If binning is not set to one of these standard modes, then the amplifier offsets and pixel delay clock will need to be re-tuned to minimize pattern noise for the desired configuration. This is a time consuming process and should be avoided until we have an opportunity to calibrate additional readout modes.

Observers should never modify binning using the WIN... option on the Xpose GUI, because doing so will not adjust the pixel delay clock and hence pattern noise will occur in the images. Instead, binning should only be changed using the options available on the CMD... menu.

CCD Readout Speeds

Use normal speed for science images. If desired, save readout time on slitmask alignments by using the (yet to be written) goifastr script to acquire quick images; this script will acquire a single image in fast mode and then return you to normal speed.

CCD Gain

[TBD: explain when to choose low vs. high gain]

Dealing With Images

Old vs. New Format

Until now, the FITS files written for both the red and blue sides were written as simple FITS format with all data assembled into a single 2-D array. To comply with accepted standards for storage of CCD mosaic image data, LRIS red and blue images are now storage as multi-HDU (header data unit) FITS files. As with HIRES and DEIMOS, data from each CCD amplifier are stored in a separate image extension. Each extension includes both data and a header describing the content of that extension. Furthermore, a primary HDU contains information common to all extensions (e.g., LRIS mechanism keywords).

Displaying images

The simplest way to display LRIS multi-HDU images is to read them into a FITS viewer which understands how to assemble mosaic data into an image. The ds9 image display tool is one such program. To view an LRIS image in ds9, simply open the image using the File > Open Other > Open Mosaic IRAF.. function. Note that you must set the ds9 flip and rotation parameters as follows in order to achieve the customary view which puts the spectral direction increasing to the right: [TBD] [TBD: note old vd. new ds9 difference]

IRAF users may use the lrisdisplay task in the keck.lris to view images on the IRAF display tool.

IDL users can use the readmhdufits routine to read the image into a 2-D array, then display it using the atv image display tool.

Reading images (IRAF/IDL)

WMKO has made available two software tools which will generate a monolithic single-HDU image (i.e., one that combines the pixels from all amplifier regions into a single-HDU FITS file) from a multi-HDU LRIS mosaic image:

Observing Strategies


Additional Notes