The Orion Molecular Cloud

The constellation of Orion is always an interesting region to photograph for amateur astronomers. A large collection of dust bands and nebulas scatters around the Orion’s Belt, the triple star in a slanted row cross the middle of the constellation. The most visible ones here are Orion’s Nebula M42. Beside it sits the running man nebula NGC 1977, resembling a man running into dust cloud. In the lower left of the image are the Flame Nebula and the Horsehead nebula in red.

This image was taken back in December 2011 when I got my brand new D7000. A total 64 minutes exposure was obtained by stacking 360 seconds individual light frames. A set of flat frames to correct vignetting and dark frames are also used in calibration. I was immediately surprised by the noiselessness and high sensitivity of D7000 compared to my old D200, which is severely hampered by amplifier glow from all corners and high shot noise because of low QE.

Orion's belt before conversion

In 2012, I had converted my D7000 into an astrophotography capable camera by replacing the color correction filter with a clear optical glass. The result is nothing but spectacular. In the following shot with the same aperture and ISO setting, a mere 18 minutes total exposure could achieve a similar signal-to-noise ratio in the H-alpha region. This only accounts for 30% exposure time comparing to the first one. And I also need to mention that the sky background is higher in the image below, which will contribute significantly to the noise in dark regions. If a comparable exposure is done with light pollution rejection filter, you could expect much better result for the image.

One caveat is that more noticeable glare and halos from bright stars, which is result of internal reflection of uncoated clear glass used in conversion. If you could obtain a 1.1mm thick glass with broadband coating, this effect will be greatly suppressed. Also you need to retain the dust filter with its IR reflecting coating. This will help you reduce the infrared spectrum from light pollution.

Chasing the Comet Panstarrs C/2011 L4

When the comet Panstarrs crossed the perihelion in early March, it has become readily visible to the astronomer in northern hemisphere. Unfortunately the weather in Indiana has been frozen for weeks without sunshine. On the 13th of March, windy weather finally clears all the clouds from horizon and gave me a chance to see it myself.

Animation from the software suggests a very low altitude angle from horizon. This means any tree could easily block your view, this is especially true for flat plain like the State of Indiana. After searching for a spot above the surrounding area, it turn out that a 20 meter slope on the bank of Route IN-52 near walmart will be the best for my first try.

The exaggerated tail from Starry Night Pro Plus really made me thought it should be visible to naked eye. Yet after almost an hour without seeing its appearance, I flicked on the liveview and began scanning the horizon. It turned out that the Panstarrs was really dim and almost soaked in the blinding twilight. And unexpectedly, the comet set into the bright glare of street lamp in the park lot.

After moving our location to the other side of parking lot, the comet is only visible between trees. I managed to capture it before it fades into the cloud. The first try is worthy enough after being blown by the wind.

Panstarrs

On 17th, my friend had led me to the Fowler Ridge Wind Farm just north of West Lafayette. A area of 20 minutes drive from center of Lafayette so unobscured that you could see the horizon. When weather clears again on that following week, we decided to chase it down once more.

Fowler Ridge Wind Farm

Sunset at Wind Farm

And here is the Panstarrs with its tail rotating to point upward. Right now this comet is fading rapidly. With the interference from the light pollution and haze on the ground, and also the twilight, Panstarrs is only visible inside viewfinder.

Panstarrs

And a finally, a short time lapse I took the other day.

IMX071 Characteristics

The IMX071 is a CMOS sensor from Nikon D7000 and D5100. Here’s a sensor characteristic test using data obtained by service mode hack.

This hack is done by Simeon on Nikon Hacker Group. By writing specific register value in USB PTP connection, the camera enters service mode where RAW sensor image can be obtained. The infamous Nikon median filter (star eater) during long exposure would also turn off. This mode is for hot/bad pixel remapping at Nikon Service Facility.

Once turned on, the sensor will be overscanned and output optical black and dummy pixels. Area definition is as follows:

Total Area: 0, 0 – 5054, 3357

Dummy: 0, 0 – 5039, 3357

Optical Black: 0, 36 – 4959, 3357

Active Pixel: 4, 70 – 4955, 3357

The column 5040..5054 are the horizontal blanking region and it outputs a constant value. The dummy pixels don’t seem to have a photodiode, hence not dark current but only read noise is contained. However, dummy pixels should not be used for read noise estimation. The optical black pixels are actual pixels with light shielding, and they can be used for read noise and dark current estimation.

First, a pair of images is taken with same exposure setting against a flat lighting source. A LCD panel display with 4 layer of parchment paper is used as uniform light source. Then the RAW image is split into 4 separate CFA channel and a center 256 x 256 uniform region is cropped.

Image pair

The average pixel value and standard deviation are recorded.

Subtract

Then the second image is subtracted from the first one, taking away the variance caused by PhotoResponse Non-Uniformity (PRNU). The rest of the variance will be the double of summation from photon shot noise, dark current shot noise and read noise. Since the shutter speed is relative fast – 1/6s, thus we ignore the dark current.

2x Std EV

The read noise can be calculated from the optical black region with the same subtraction. Then the variance of read noise is subtracted from the rest. The following table summarize the characteristic at ISO 100.

ADU ISO 100 e-
AVERAGE STD DEV 2 RN 2 STD DEV Gain(e/ADU) STD PRNU READ NOISE FWC PRNU (%)
1 R 5742.589 71.602 1.05 54.746 2.241 20.812 1.7 36709 0.362
2 Gr 6767.172 71.968 1.016 2.614 1.9 41392
3 Gb 6790.208 72.343 1.014 56.048 2.595 22.893 1.9 41103 0.337
4 B 4522.246 64.144 1.027 48.005 2.199 15.708 1.6 36023 0.347

A digital multiplication is applied to Red and Blue channel, thus the sensor full well is roughly 42ke- at ISO 100. Read noise is really low, 2~3e-. Note that “DEV 2” are the summation of 2 deviation resulting from image subtraction.

Dark Current

Later, the dark current is also estimated from optical black region, yielding 15 ADU in total or ~0.14eps (electron per pixel per second) at 21°C. When cooled to outside temperature at -1°C, dark current falls to roughly 0.007eps. The doubling temperature is less than 6.5°C.

The preliminary testing suggest the Exmor CMOS is much better than previous generation interline SuperHAD CCD. More accurate testing can be done with complete Photon Transfer Curve once the black level correction is hacked in the future.

Compilation of libgphoto2 under Cygwin

Gphoto2, and its library libgphoto2 is a Linux application enables controlling cameras and downloading images through USB PTP or serial cable. It is of importance if you would like to build a remote controlled camera or automate the time lapse photography with advanced setting, such as altering the shutter speed during sunset with a predefined value, or make exposure at precise moment for solar eclipse. Another feature will be turning on service mode to enable uncooked RAW image download for Nikon DSLRs. Cameras from almost all vendor are supported.

But this package is for Linux, we will need a emulator to work in Windows. Cygwin is one great linux emulator with a core cygwin1.dll to link basic windows API with the Linux API. Application compiled in Cygwin will be saved as a Windows executable (.exe), and can be run from Cygwin command line or directly in windows with DLLs in the same folder. To help newbie who don’t know much about Linux and want quick compilation, here’s a list of package you need to install in order to get a working libgphoto2.

I’m working with the following combination. Unlike Windows and Mac, Linux is a collection of open source package, compatibility is really a big issue. It’s like in the old days when they quote TIFF as Thousands of Incompatible File Format!

Cygwin Setup v2.774 & libgphoto2 v2.5.1.1

 

autoconf

libtool

pkg-config

GNU make

libusb

gcc-g77

libiconv

gettext

 

Except for “GNU make”, make sure you installed the source code for the other packages. Then it should be fine to follow the install procedure.

Peeping into Pixel – A micrograph of CMOS sensor

Macro-photography are done at 1x ~ 2x magnification. Microscope on the other hand could easily deliver a 40x magnification without eyepiece. In this post, we are peeping into the basic element that captures the image in digital photograph – a pixel on CMOS sensor. I had obtained a Nikon JFET LBCAST sensor from a broken D2H imaging board. LBCAST is still based on CMOS fabrication technology and it’s an Active Pixel Sensor.

Photographing an opaque sample compared to biological slice is extremely difficult, since ordinary trans-illumination will not work. An epi-illumination, de facto illuminating through the objective, should be used instead. Basically a half mirror is in place of the optical path to direct light towards the objective, then back in to the eyepiece and camera. Epi-fluorescence will use a dichroic mirror and a pair of filters.

LBCAST

Back Side

Cover Glass

The D2H sensor die is sitting inside a robust 38 pin ceramic dual-in-line package. But the bonding wire is shielded by a metal frame underneath the cover glass, thus made it impossible to see the die marking. These’s no package marking on the backside except a tape indicating its serial number (or could be color correction information used for calibration). The cover glass is rather thick, roughly 0.7mm.

Top Left

Top Right

Bottom Right

The corner has clearly shown the active pixel region covered by optical black and non-microlensed region. This image is taken by a 10x objective on a stereo microscope. Now we peep in using 40x objective!

Effective Pixel

The effective pixel array (Note that the periphery of the active region will be discarded due to color interpolation and results in the effective pixel region)

Unfortunately the camera is B/W. The brighter ones are green pixels while darker ones are red and blue. With this resolution, we can actually calculate the optical fill factor, it’s well below 60% given such a big lens gap! Even though a square microlens seemed to be employed, not all light is directed into the window. It seems the microlens array are not fabricated in one cycle, as you notice the lenslet on blue and red pixel are slightly larger then green lenslet.

Optical Black

Now comes the optical black (OB) region, and the edge of active pixels. The optical black pixels have a metal shielding in the photodiode window. By blocking light, it will only output dark current and bias level, which will be used as black reference for active pixel region. Nikon subtract the average value of OB from the intensity value in active pixel region, which transforms the black level to 0. This is not good for astrophotography and Canon will add a 1024 ADU to it. From OB pixels, it becomes even clear that only a partial region of the microlens is illuminated, roughly 40%. I believe that’s the reason for low QE, and as a result, low 18% SNR in D2H.

Lens Array border

Finally comes to the border of lens array, now you have bare Color Filter Array (CFA) above pixel. You can clearly see the metal lines (column lines; the sensor is oriented 90°) running in between, which occupies a lot of space and is also the reason in need of microlens.

Wiring

The very corner of the total pixel array (Oriented 90°). Each row has 2 control lines, a JFET select/reset line and a photodiode transfer line. The GND is the metal layer 2 above the row, not visible here. The column line situates in between as metal layer 1 according to this paper, which is the signal out, and it is really thick to reduce resistance!

Another interesting observation is the lack of blurring function of this cover glass. Canon has integrated its second anti-aliasing layer of OLPF as sensor cover glass in full frame and new generation APS-C DSLRs. Apparently the OLPF stack is standalone in D2H.

Column Out

Moving the view to right side gives you the column circuit, possibly the buffer, CDS and column scanning driver that latches to the output amplifier. Note a 4 in mirror image being photo-lithographed on the die, this indicates the column 40. The die also has a "+" in every 5 columns in between.

Corner

The opposite long edge of the sensor. (Image in 10x) Even though some of the non-microlensed pixels are hiding beneath the metal frame, we can still see the column number from 3, 4, 5…

Last Line

Mirror the image at the other corner, the last line is 256, which indicates total of 2560 columns.

Line 390

Somewhere between column 385 to 405, there’s a recess in the long edge. I’m not sure what this for. (Image in 10x)

LBCAST-XRay

The ceramic package viewed through a X-Ray scanner showing the bonding wires linking the lead and die. The metal frame is also visible.

Very interesting right, huh? Now we can compare it against a Micron CMOS sensor (Now Aptina) with 5.2um pixel.

Micron 1300

Die marking MI-1300 from year 2002, MT9M001.

MI-1300 Microlens

Now the microlens itself. We can clearly see a much narrower lens gap and higher fill factor. This sensor boost a 55% peak QE, but still less than the Sony Exmor sensors. I hope someone can donate me one for dissection.

The contributor behind the scene – Olympus LUC PL FLN 40x objective. This objective is designed for inverted microscope and has a collar to set the glass slide thickness, allowing the compensation of chromatic and spherical aberration.

Updated: 2/12/2013

First test of converted D7000

Right now the camera is fully capable of capturing the scarce H-Alpha light from the deep universe.

Last night I went out for a test aiming the camera with 180mm lens at the center of Cygnus. Aperture is set to F3.5 to limit chromatic aberration. Tracking is done with AstroTrac TT-320X. Total exposure 33 minutes.

Picture saved with settings embedded.

Nikon D7000 H-Alpha Conversion

It has long been recognized as Nikon DSLRs are boosted by Sony sensors since D100. Now in the 3rd generation cameras, Nikon switch to Sony Exmor CMOS sensor from HAD CCDs. These CMOS sensor utilized on-chip column parallel Analog-to-Digital Converters (ADC) running at very low clock rate around 20kHz compared to serial external ADC that runs at around 10MHz (Such as D3/D700/D3s and Canon DSLRs. Calculation as follows: 12.2MP x 9FPS / 12 Channel = 9.2MP/ (Second x Channel) ). The slower clock rate and integration of ADC on chip significantly reduces read noise, as it would be beneficial for dynamic range.

The latest of all, D7000, has been analyzed by Chipworks and they had found a Sony IMX071 Exmor sensor within. Test done by Dxomark indicated increased sensitivity compared to previous CMOS sensor (D90 and D300s). Interestingly, either Nikon nor Sony advertise their gapless microlens structure as Canon always did, but it has been clearly revealed that IMX071 microlens array does not have gaps in between. (Fig 1)

IMX071 5D vs 5Dii

Figure 1. Chipworks teardown shown pixel vertical structure. Above: IMX071 gapless microlens. Below: Canon 5D and Canon 5D Mark II

Combination of significantly improved Quantum Efficiency (QE), lowered read noise and dark current at room temperature against CCDs, these DSLRs should be highly competent in astrophotography. However, one more obstacle remains: DSLR are not sensitive to hydrogen alpha line (656nm) from most of the emission nebulas simply because camera manufacture add on a color correction filter to mimic the response of human eye. This color correction filter absorb a large proportion of red  and almost all infrared photons while leaving green and blue channel untouched. The silicon based sensor itself are highly sensitive in the entire visible spectrum ranging from 400 to 700nm, and extending towards near infrared of 1100nm with much lower response. So the simple answer to this is remove it!

 

Warning!

Please use this instruction at your own risk! I will not be responsible if you accidentally break your camera in the process! If you have shaky hands and are not confident with doing this yourself, send it to a qualified company for conversion or don’t do it!

 

Filter Structure

But removing it cause another problem when large amount of infrared rushes towards the sensor, then how do we solve it? So let’s take a look the filter in detail.

Actually the filter is more complicated, it consists of 2 parts: a dust reduction filter, and a sandwich of 3 layers of glass stitched together. The later is usually called ICF (infrared cut filter), or sometimes by its other property – Anti-aliasing filter, or optical low pass filter (OLPF). Each layer has its own function. This filter stack not only serve to suppress infrared leakage and correction of color in red channel, but blurs the image on pixel level to reduce the color moiré inherited in Bayer sensor. The dust reduction filter and the last layer of ICF are both similar in thickness and are made of birefringent material. And the first layer of ICF is a wave plate similar to the one in your circular polarizing filter. When oriented 90° to each other in conjunction with the wave plate, they separated the light in horizontal and vertical direction respectively, translating one dot into 4 and thus blur the image. The thickness of both are tuned according to the pixel pitch. As a general rule, the bigger the pixel, more blur you need and thicker the birefringent layers.

D7000 sensor module showing inner filter stack on top and a dust reduction filter disassembled on right.

The middle layer in the ICF is the color correction filter that absorb deep red photons and infrared. Another thing to notice is the dust reduction glass is coated with an interference filter that blocks UV and IR. The sharp cutoff allows greater than 95% of visible spectrum between 430 to 680nm to pass through. So in this modification, we will only remove the 3 layers ICF stack while preserving the dust reduction filter that blocks UV/IR as well as keeping dust away. Removing this filter also change the infinity focus distance and you may not be able to achieve focus at infinity for some lenses. So I ordered a clear piece of optical glass with 1mm thick just in case.

 

Modification

The detailed disassembly step can be found at Lifepixel website: http://www.lifepixel.com/tutorials/infrared-diy-tutorials/nikon-d7000-ir

Before tearing down your camera, prepare the small boxes for preserving the screws. I used the petri dish to help me memorize the same batch of screws from the same panel. Duct tape can also help you organize the screws. Also be sure to ground yourself and not to do it during cold and dry winter to prevent static charge from damaging the delicate electronics inside. The screwdriver you need is #000 or 5/64" Phillips type. Do not use flash before conversion nor open the flash. This will charge the capacitor and may give you an electrical shock once you touch it, or destroy the circuit when you accidentally short circuit inside.

The disassembly step are as follows:

1. Remove battery, eyepiece rubber cap and SD cards. Remove the lens and cap the body.

2. Unscrew and remove the bottom panel

Bottom Removed Bottom Panel

Bottom panel removed and it is made of plastic

3. Unscrew the ones on SD slot compartment, viewfinder, one on the left and 3 silver ones in the bottom. Gently lift LCD panel unit.

Back Panel Main PCB

The back panel is made of magnesium alloy.

4. Carefully flip the hinge connector using your finger nail or a forceps and gently release the ribbon cable from the slot. Be sure to identify which part is the rotating bar and which fixed jack. This is the most crucial and tricky step and you need to be really careful when dealing with these flat cables. Make sure all the cable are properly released before the next step.

Toshiba CPU Ribbon Cable Disconnect

The main PCB with Toshiba microcontroller chip. Ribbon cable are disconnected.

5. Unscrew the 6 silver screws on the PCB. Lift the PCB from right side and slowly pull the PCB to the right since the USB/HDMI jack is inserted into the plastic panel on the left of the camera.

Main PCB Backside CMOS PCB

The back side of PCB, where the virtual horizon sensor is in the bottom right corner. Removing the PCB exposes the sensor frame. The sensor power supply cable is L shape and the sensor output in 8 LVDS channels (+1 for Clock) to the main PCB.

6. Now it’s time to access the sensor. From this step on, you should consider dust and your dirty hands very seriously. I’m converting in a laboratory fume hood and wear latex gloves from this step onwards. The 3 big silver screw in the above image fasten the sensor module to the fore body of the camera. Once you tweak it, the focus calibration is no longer valid. To proceed, release the last ribbon cable and unscrew the sensor board. I suggest you mark the screws with color marker pen to distinguish the screw with its mounting hole, as well as its preset rotation position.

 

Marking

Mark the screw before proceed. The CMOS sensor is driven by a 54MHz crystal oscillator.

Working in hood

Now move to the hood

Sensor before Shutter

The sensor module and the shutter blades

7. The piezoelectric elements attached to the dust filter is connected via ribbon cable as well. But we do not need to desolder it. Unscrew the 4 holding the dust filter to the sensor unit and gently lift the dust filter frame (2 more on the right side in hidden below the aluminum foil). Once the screws come loose, gently lift the dust filter. Use the forceps to lift one corner of ICF and take it out. Reverse the steps and assemble your camera.

Sensor after conversion

After removal, sensor became much more transparent

 

ICF Structure

ICF/OLPF Diamension

The dimension of stack is 29.50mm x 25.30mm measured with a vernier scale. The wave plate and color correction filter is a little bit smaller, giving a 21.50mm in height. This dimension has been standard for Nikon since D70. The thickness reading from a micrometer yields a 1.182±0.002mm for the entire stack and 0.538±0.003mm for the transparent anti-aliasing glass. This means the color correction filter and wave plate is 0.64mm thick, which is identical to that in D90.

ICF

The cross section of ICF stack under microscope, showing 3 layers of wave plate, color correction layer and birefringent glass from bottom to top. The top is facing the CMOS sensor.

 

Focus Shift

Since we did not replace the ICF stack with a clear sheet of glass of equivalent optical depth, the camera now will become significantly nearsighted, and the phase detection focus will be useless. In my test, I set both lens and default focus fine tune to +20. The result is still slightly blurred. And for lenses with hard infinity focus stop, it will become impossible to achieve sharp focus at distance. Right now the only lens I have that can obtain focus at infinity is AF 180 2.8D, for this lens has to have a large tolerance of infinity for its focus shift of ED elements dependent on temperature variation.

Infinity after conversion

The Liveview infinity manual focus position largely deviates from original infinity focus, where bar should point right in the middle of the "\infty"

My 18-105 DX seems to achieve infinity focus at zoom range greater than 30mm but not the wide angle end.

 

Sharpness Test

The removal of of ICF along with its anti-aliasing filter should increase the resolution on the pixel scale. This is in principle similar to recently announced D800E. However, as we had preserved the first AA layer for its IR rejection coating and dust reduction, this camera will have astigmatic vision. The images below are shot at ISO12233 chart at 70mm and fixed distance using liveview focus. NEF raw is taken and demosaic using MaxIM DL. These section are cropped at 200% from the same image.

After V

After H

After conversion, the vertical resolution is increased compared to horizontal. And the horizontal resolution remained the same (See below)

 

Before V

Before H

Before conversion, resolution is the same on 2 directions.

This test suggests that the dust filter separates the image on horizontal direction and the last layer of ICF blurs the vertical one.

 

OLPF under microscope

To investigate under a microscope, the last transparent layer of ICF stack is place between a hemocytometer and 40x objective. The image below clearly illustrate the effect of the OLPF layer with a directional blurring of vertical lines. As ICF stack is placed with long edge parallel to the vertical lines, its definitive proof of vertical burring function of the OLPF layer.

ICF under Microscope

Left: with OLPF; Right: without. The distance between 2 lines in a square is 50um.

 

Clear glass replacement

Now in order to achieve infinity focus for my 18-105 lens, I’m going to replace the ICF with a clear optical glass. One way to test if the optical depth differences is simply to use a microscope. Place a sheet of paper underneath the filter and focus the microscope at 200x on the thin fiber on the paper. Then gentle replace it with the new optical glass. If the focus is sharp, then at least this means the focus remained the similar. The rest of the error will be within the range of D7000’s focus fine tune system.

The replacement HK-9 glass with a APS-C sensor as size comparison

Bonding Wire

Notice the bonding wire is sufficiently different from IMX038, where a lot of camera website used the wrong photo for this sensor. (Click for large image)

The procedure is the same, just place the glass in the same rubber gasket frame using forceps.

Clear glass on sensor

The rubber gasket sits on the IMX071 Sony CMOS sensor

 

This replacement glass lacks anti-reflection coating. The thickness is 40.3 Mil or 1.023mm. HK-9 glass is equivalent to BK-7 borosilicate glass with a refractive index of 1.5. After replacement, The focus almost comes back to the original factory setting.

 

Transmission Analysis

To roughly assess the transmission, I used the same lens setting to infinity focus and take a RAW image of 1/5s exposure at the LCD screen with the same aperture, ISO and the maximum brightness setting of LCD panel. The table below shows the raw average ADU count in the center uniformed area of image, and the ratio is normalized to ICF removal one.

RAW ADU

Ratio

R

G

B

R

G

B

Before

5738

11257

7947

0.51

0.86

0.92

ICF Remove

11308

13114

8643

1.00

1.00

1.00

HK-9

10651

12312

7966

0.94

0.94

0.92

It is astonishing that we have almost 1 fold gain in the red channel. The green channel is also improved a little. Note that HK-9 reflect and absorb 6-8% light in all channel.

 

Color Correction Filter Spectrum Property

Since gaining 1 fold more red light in a channel doesn’t mean the distribution of that gain is equal at different wavelength within. Here we use a UV-VIS spectrophotometer to measure the transmission profile of the infrared absorbing glass.

Transmission Spectrum

Transmission property of ICF, replacement glass and a quartz glass window (RCP) from 200 to 900nm. Actually I doubt the replacement glass as HK-9 will strongly absorb at 300nm, and the transmission curve closely resembles N-BK7 glass. Also notice that an uncoated glass window will reflect 8% of light in total on 2 interfaces. The quartz filter is broadband coated, which bring the transmittance up to >96%. The quartz is transparent down to 160~180nm in UV below the detection range of this spectrophotometer.

After all, this means we had a 4 fold gain at 656nm Ha emission line plus an increased QE of new generation sensor, personally I’m well satisfied with this result.

 

Updated 1/22/2013

Follow

Get every new post delivered to your Inbox.