Jump to content
rew

My trilobite of the week photography

Recommended Posts

rew

I started the "My trilobite of the week" thread in the Members Collections section as a way of getting myself to actually start photographing my fossils for the web site I am creating.  I have many different types of fossils, but I only collect fossils from before the dinosaurs so that means lots of Paleozoic fossils and most of the ones I have are trilobites.  As you would expect for a project like this I have been learning as I have been going along.  I got my photography equipment for the specific purpose of photographing my fossils, so I have a different set of lenses than I'd have if I was doing photojournalism or wildlife photography.  Most of my fossils are small, and nothing is bigger than a couple of feet long.

 

The hardware:  Canon EOS 5D Mark III camera.

Canon 24-70 mm zoom lens.  This is my most "ordinary" lens and the one least used.  For pictures of big fossils and of visiting humans.

Canon 100 mm macro lens.  This is the main workhorse.  Most of the trilobites are photographed with this lens.

Canon MP-E 65 mm magnifying macro lens.  This has no focusing ring, but has a 1 - 5x magnification ring.  For small stuff, like agnostid trilobites.

Cognisys Stackshot focusing rail.  This is a focusing rail driven by a stepping motor.  There is a little control box so you can control it manually but the normal operation is to plug it into a computer with a USB connector and control it by software.  A focusing rail is essential for the MP-E magnifying macro lens and useful for the other macro lens.

Two flashpoint LED photography lights, 4000K color temperature.  These are big square arrays of LEDs, I put one on each side of the specimen to keep shadows to a minimum.

A tripod.  The focusing rail is attached to the tripod and the camera is attached to the focusing rail.

 

I needed a way to get straight on dorsal shots.  If the trilobite is flat on a table this is hard to do, I'd need some fancy hardware to point the camera straight down.  So I made a 45 degree table with a ledge on it.  I lay the trilobite on the table and point the lens down at a 45 degree angle, and get a straight on shot.  The table was actually made from Styrofoam board I got at Staples.  It's light as a feather, and sturdy enough for trilobites but I wouldn't put a dinosaur femur on it.

 

If you've ever done macro photography you know the depth of field is very small.  If you want the entirety of a 3D trilobite to be in focus you have two options.  The first is to use a small aperture, say 24 or higher..  This increases the depth of field at the cost of some resolution and of much less light coming into the camera.  The latter issue may not be too much of a problem -- the fossil isn't going anywhere, so you can simply use a longer exposure.  The second option is to use photo stacking, which is what I actually do.  In this case a series of photographs are taken at different distances from the subject, and the "in focus" parts are combined by software into one picture.  Of course each picture is taken from a slightly different perspective so part of what the software has to do is pick is single reference point and map the pixels from each photograph into that single perspective.  So, the software I use is:

 

Helicon Remote -- controls the camera and the focus rail.  This has a USB connection to both the camera and the focusing rail.  This is used to take a series of photographs at different distances from the subject.

 

Helicon Focus -- combines a series of photographs taken with Helicon Remote into a single in-focus-everywhere photograph.

 

GIMP -- the poor man's Photoshop.  Ideally the photos will be done right enough that all I have to do is attach the metadata copyright, and crop and/or rotate the picture.  Unfortunately sometimes this ideal isn't met.

 

DarkTable -- I use this solely to convert raw files to TIFF files.

 

The photos from the camera are stored as raw files, Helicon Focus can work with raw files.  It converts them internally into TIFF files when it processes them.

 

To be continued....

 

 

 

Share this post


Link to post
Share on other sites
KathyW

"For pictures of big fossils and of visiting humans."

At our age, with family visits, that's "visiting fosslls".  (I'm REW's sister).

Edited by KathyW

Share this post


Link to post
Share on other sites
rew

Feh, I'm not a fossil yet.  But some day some paleo-anthropologists will dig up my bones to find out what sort of hominid occupied the ancient land of Usa.

Share this post


Link to post
Share on other sites
rew

Parameters, part 1.

 

I set ISO to 100.  This gives maximum resolution and minimum light sensitivity.  I can always deal with the latter by using a longer exposure.

 

What about aperture?  My standard setting is 7.1, which gives good resolution but only has a small strip of the image that is fully in focus.  The first image was done with aperture 7.1 and the second was done with aperture 32, the maximum allowed with my 100 mm macro lens.  Note that a very long exposure was needed for the second picture.  It is clear that more of the image is in focus with aperture 32, but even so neither the spine at the pygidium nor the very front of the trilobite are in good focus.  That is why I use aperture 7.1 with photo stacking.

 

apertue-7.1-cropped-small.jpg

aperture-32-cropped-small.jpg

aperture-32-cropped-tail.jpg

aperture-32-cropped-front.jpg

Share this post


Link to post
Share on other sites
rew

Parameters, part 2.

 

What about exposure time?  Originally I just used the camera's auto exposure feature.  But Helicon Focus kept complaining, because sometimes the auto setting would change the exposure from one image to the next and this would make it hard to match up the images.  One consequence of this would be bad color balance.  So now I set the exposure manually.  I actually do multiple runs at several different exposures, and then pick the one I like best.  While some images are washed out and obviously over exposed, and others are dark and dim and underexposed, there's a broad range in between where it's a matter of subjective judgement about which is better.

 

What about color balance?  I still leave this to the camera's automatic color balancing algorithm.  The preset values are useless -- I'm not doing the photography in sunlight, or under an incandescent light, and there is no option for 4000K LEDs.  When I tried setting the color balance manually I always got horrible results much worse than the automatic algorithm, which, most of the time, is pretty good.  My main gripe is that there is a tendency for gray trilobites on gray rocks to come out too reddish, if that happens there isn't much I can do but try to tone it down in GIMP.

 

 

Share this post


Link to post
Share on other sites
rew

Helicon Remote works well.  You can set all the usual camera parameters (exposure, aperture, ISO, etc.) and there are buttons to move the focusing rail back and forth so you can set the "A" point (furthest away from the subject) and the B point (closest to the subject) and specify the distance between photographs.  You hit "start" and then it's "click...rrrrr...click...rrrr....click....rrrr..." as Helicon Remote takes pictures and moves the camera to the next position.   The main screen shows what the camera sees so you can see what's in focus.  My only gripe is that if you turn off the camera (to change the battery, for example) and then turn it on again Helicon Remote doesn't see the camera again -- you have to restart the program before it sees that the camera is attached.  That means you have to remember the A and B information and any other parameters before you restart the program.  This is a minor complaint.

 

Helicon Focus has three algorithms for combining the pictures.  I don't use Method A, occasionally use Method B, and mostly use Method C.  Method B gives very good results for very flat specimens, like the Bristolia insolens.  Method C is the only algorithm that works well for highly three dimensional specimens, where as the camera moves different parts of the the objects in the background become occluded or no longer occluded by objects in the foreground.  This not only applies to spiny trilobites but to typical proetids as well -- they may be small and spineless, but are still highly 3D, like the Proetina ihmadii I recently posted.  Helicon Focus normally works very well, but there are some glitches and gotchas. 

Share this post


Link to post
Share on other sites
rew

Hot Pixels From Hell

 

Here is a problem that bedeviled me for some time, and which I have only recently got resolved in a satisfactory way.

 

When zoomed in I often see streaks of brightly colored pixels on the images.  See the included images.  Helicon support told me that these were due to "hot pixels" -- pixels on the sensor that were stuck on to one color or the other.  Apparently even high end cameras always have some bad pixels.  In single shot photography each hot pixel is surrounded by hundreds of thousands of good pixels, so you're not likely to ever notice them.  But when combining a sequence of images there can be a long series of photos where the same hot pixel is in the "in focus" part of the image so gets replicated many times at slightly different positions in the combined image.  Thus the pixel streaks.

 

While the streaks can be eliminated with the use of the "clone" tool in GIMP that's a lot of work and I hate doctoring up my photos in this way.   Helicon support said the hot pixels could be eliminated with the dust map feature.  A dust map is used to deal with the problem where dust gets on the sensor, blacking out some pixels.  You take a picture against a plain white background to get an image of the dust, which is loaded as a dust map.  The algorithm avoids the dark pixels in the dust map.  For hot pixels they suggested the opposite -- take a picture with the lens cap on, so the hot pixels show up as bright areas against a black background.  When I tried using such a photo as a dust map it didn't work at all.  Here's what finally did work.

 

I looked at several of my Helicon Focus produced images in zoomed in mode and found all the pixel streaks created, noting their locations.  Keep in mind that when you see a pixel streak none of the pixels you see will be at the exact location of the bad pixel in a raw file, because of the coordinate transformations needed to get all the in focus pixels into a single perspective.  For each streak I found a raw file that was in focus for the region where the pixel streak occurred and looked at its TIFF file (you can't view raw files directly, software that lets you see raw files does so by converting them to TIFF files first).  I'd zoom in and hunt around until I found the offending bad pixel, and noted its location.  In this way I found all the bad pixels.  You might think we're done -- create a TIFF file that is black everywhere expect for white pixels at the bad pixels, and use that as the dust map instead of the lens cap picture.  Well that doesn't work either.  The TIFF files I looked at, created from the raw files with DarkTable,  were 5794 x 3868 pixels in size.  But Helicon Focus uses a different raw convertor and its TIFF files are of different size.  Helicon support told me that Helicon Focus puts its TIFF files in C:/Users/rew/ AppData/Local/Temp/Helicon and looking there I saw that the files are of size 5760 x 3840.  The dust map must be of the same size as the TIFF files Helicon uses so must also be 5760 x 3840.  This leads to the question -- how do I map coordinates in my DarkTable TIFF files to the TIFF files used by Helicon Focus?  By looking for a couple of bad pixels in the Helicon TIFF files and comparing them to where they were in the DarkTable Tiff files I determined that the transformation is (x, y) -> (x - 16, y - 14).  So, for example, a hot pixel found in a DarkTable TIFF file at (1642, 1129) becomes a white pixel in the dust map at (1626, 1115) .  When I created a dust map this way and used it the pixel streaks finally went away.

hot-pixels.jpg

hot-pixels2.jpg

Share this post


Link to post
Share on other sites
rew

BTW, it is common for a "hot pixel" to show itself as a 5 pixel cross -- a bright pixel in the center and four adjacent pixels that aren't quite as bright.  This is apparently due to some sort of averaging of adjacent pixels; I don't know if it happens at the hardware or the software level.  But I determined empirically that you only need to put the center pixel in the dust map to make the pixel streaks go away.

Share this post


Link to post
Share on other sites
rew

The Ghost Spine Problem

 

Most of the time Helicon Focus' Method C works well for 3 dimensional trilobites.  But there are some spiny trilobites that defeat the algorithm.  Koneprusia dahmani was one such trilobite.  The dorsal shot came out well.  But the shot of the left side, necessary to show the down spines with their cross spines, didn't work out too well.  The problem is due to the long spines on the left side that extend towards the camera.  They are well in the foreground of the rest of the trilobite, although I was careful to set the A and B points so that in focus pictures were made of all parts of the trilobite.  The close up in the third picture shows the problem.  Several of those left spines have become semi-transparent, so you can see parts of the spines, thorax, and background of the trilobite through them that should be occluded by them.

dorsal-cleaned-cropped-rotated-small.jpg

left-small.jpg

transparent-spines-small.jpg

Share this post


Link to post
Share on other sites
rew

There's no elegant fix to this glitch.  Drastic surgery is required.  I took another series of left side photos, with a gray piece of paper behind the forward spines and in front of the center spines.  This is a nail biting operation when you have an expensive trilobite with delicate spines.  Exactly the same A and B points as before were used so as to make sure that image would be exactly the same size and in exactly the same position as the original image.  Note that with a plain solid background the forward spines are solid, not transparent.  I loaded the result into GIMP, zoomed in, and for each of the ghost spines I carefully selected the spine against the gray background.  Then I used the GIMP "Paste into Selection in place" function to copy the selected spine into the original left side image in the same spot that it came from.  Finally, minor discrepancies at the join between the original and pasted in spine were cleaned up with clone.  Why did I use gray paper rather than white paper?  Because white paper reflects too much light back onto the spines, and they look too light when pasted into the original.  The final result looked pretty good, but it feels like cheating to have to do this. 

 

I reported the ghost spine problem as a bug to Helicon but there engineer said that this was just too extreme a case for the algorithm.  I'd like to see a Method D that can handle cases like this, but I don't know if their other customers have this problem.

left-blocked-small.jpg

left-cleaned-patched-cropped-small.jpg

Share this post


Link to post
Share on other sites
rew

Now you know everything I know about photographing trilobites.

Share this post


Link to post
Share on other sites

Create an account or sign in to comment

You need to be a member in order to leave a comment

Create an account

Sign up for a new account in our community. It's easy!

Register a new account

Sign in

Already have an account? Sign in here.

Sign In Now


  • Recently Browsing   0 members

    No registered users viewing this page.

×