Observation 91801: Alectoria imshaugii Brodo & D. Hawksw.
When: 2012-04-04
Herbarium specimen reported

Notes: note “isidia-like” spinules

easily distiguished from Usnea as lacking a central chord

this was on Pseudotsuga menziesii close to Chiwaukum Creek a few miles up trail #1571 (need to find my specimen with data)

very beautiful forest with many fine flowers, including lots of Corllorhiza maculate, Calochortus lyallii, and the endemic Lewisia tweedyi (serpentine soil)

used focus stacking – see notes with photos

Species Lists

Images

210419
these were shot at home of the specimen collected 4 days previous, using 90mm macro, LED headlamp which sometimes I use for light source (works well for affordable source for dissecting scope too) – the actual color should not be such a harsh white
210422
210423
focus stacking software Helicon Focus in process – guess its choosing which portions of each exposure to use – just thought it was interesting
210657
this screen shot was made some time after the previous one posted

Proposed Names

83% (1)
Eye3 Eyes3
Recognized by sight
Used references: McCune, Bruce, and Geiser, Linda (2009) Macrolichens of the Pacific Northwest, Goward, Trevor (1999) The Lichens of British Columbia, Illustrated Keys, Part 2 – Fruticose Species

Please login to propose your own names and vote on existing names.

Eye3 = Observer’s choice
Eyes3 = Current consensus

Comments

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I’ve tried stacking micrographs, too
By: Jason Hollinger (jason)
2012-06-01 00:24:40 PDT (-0700)

No dice. I think the problem is you’re looking at a translucent object, so there is equal detail throughout each frame. How can it know which particular focus depth you want to use for each object? But fortunately, since it’s so blurry and “messy” anyway, it’s easy to get it to look okay even by hand.

more on DOF stacking
By: Richard Droker (wanderflechten)
2012-05-31 17:20:13 PDT (-0700)

Came across these software comparisons which make me want to try Zerene.

Look at the series of flower photos at http://www.flickr.com/photos/54925614@N08/tags/helicon/

Lately I’ve been using the clone stamp tool on images of apothecial sections to combine asci which are in better focus on different images. It can work quite well. (Helicon stacking doesn’t really work, probably due to too much going on with asci and paraphyses.)

sorry if misleading
By: Richard Droker (wanderflechten)
2012-04-05 17:42:52 PDT (-0700)

Came back to edit my comment but you were too fast. Wanted to say sorry if initial depth map was misleading.

I hear you!
By: Jason Hollinger (jason)
2012-04-05 17:28:44 PDT (-0700)

Rest assured your “not as good as should be possible” is still better than anything I can produce no matter how much time I spend on it! :)

(The black and white outline I was concerned about is hardly visible in the new screen shot, by the way. So much for my theory. :)

eventually Helicon went through a stack of 8
By: Richard Droker (wanderflechten)
2012-04-05 17:24:44 PDT (-0700)

Although as a photographer these questions really concern me I just haven’t had time to go very far with them in the past and had decided to accept “not as good as should be possible” for the time being. There were 8 photos in the stack (see newly posted image), but I don’t know how many of these had been processed at the time I made the screen shot (which didn’t include the information on the right margin) of the depth map previously posted.

Width of branch is much less than distance between branches
By: Jason Hollinger (jason)
2012-04-05 13:57:57 PDT (-0700)

But I see your point, it does look like only a few photos are in this stack, so that must account for it.

Braches are round
By: amadej trnkoczy (amadej)
2012-04-05 13:46:16 PDT (-0700)

Jason I don’t believe moving of the object is the problem. Braches are round in cross section. So, the ‘front’ section is at a different focal plane than edges. The program takes into account the focal plane, which shows the highest sharpness. This means that central part and edges of a branche in a final picture come from two different pictures. This is shown as white margin around gray/black branches in the depth map picture.

Richard, how many pictures you had in the stack? Are they four?

comment about depth map
By: Jason Hollinger (jason)
2012-04-05 13:21:55 PDT (-0700)

Looking at your depth map, I see a number of branches have black and/or white borders. This can’t be ideal. I wonder if that is evidence of the thallus moving a little during your shoot? Just a thought…

Oh. My. God.
By: Jason Hollinger (jason)
2012-04-05 13:19:45 PDT (-0700)

I’m so out of my league!

The slider is critical, isn’t it? I’ve got to get my hands on one of those before I have a prayer.

Still, I was having trouble with imperceptible movement of the subject. I have to hold my breath and everything, and it still would shift enough to cause screwy edge effects. Maybe Helicon does a better job with registration. But I wonder if this is why your photos “never seem quite as good as expected”? It would especially be a problem with hair lichens like this Alectoria (but not crusts).

There seem to be three different ways of advancing the focal plane: adjusting focus, adjusting zoom, and moving the camera closer. Moving the camera is how my dissecting microscope stacking set up works, and this is fine for 30x, but it causes radial streaking effects at 10x (larger depth of field). Problem is that parts of the subject shift with respect to other parts in the foreground or background. Maybe this is minimized by clamping down on the aperture and taking a bazillion shots (which you can arrange easily if you have an automated slider). Still, I would expect the other two methods to work better. In either case, your stacker program has to adjust either for slow drift in exposure (adjusting focus) or in magnification (adjusting zoom). There are probably whole forums and papers devoted to this, aren’t there? :)

my setup
By: Richard Droker (wanderflechten)
2012-04-05 12:49:15 PDT (-0700)

My setups are sort of Rube Goldberg. For this one I grabbed the base of the lichen with longish forceps which were then held closed with a rubber band. The forceps were then attached with a rubber band lengthwise to a short 2 by 4 which was placed horizontally on a stack of 3 or 4 books, so height was adjustable by adding or subtracting books. After the camera was in the right place a black section of mat board was positioned as background. (If there is no wind I can do this outdoors with a more natural background.) When focus stacking I usually shoot at f16. I “expose to the right” (of the histogram), locking the mirror and very carefully moving the camera on a macro slider (photo at http://www.flickr.com/photos/29750062@N06/5674759830/ ). (Actually I don’t know if this works better than changing the focus with the lens, but that will also change the effective f-stop.) (After playing around with Helicon Focus I settled down to using Method B (Depth Map) with radius 3 and smoothing 2. Probably should customize settings for particular subjects, but that would take a long time.) I use 1 or 2 headlamps mounted with rubber bands on upright short 2 by 4s (also handy for use with my dissecting scope, and even with the compound scope on occasion, e.g. for apothecial sections in reflected light). (Outside my light source is the sky (without direct sun) and a folded white mat board (open book) for reflecting diffuse light. For propping up crusts I have a collection of small objects of various shapes (wedges are useful). Erasers are good because they don’t slip.

Usually this doesn’t take too long, although the final image never seems quite as good as expected.

Beautiful!
By: Jason Hollinger (jason)
2012-04-04 19:33:24 PDT (-0700)

So, I’ve been wanting to ask this for a long time, now’s my opportunity: how did you do the physical setup? How do you hold the specimen steady? How do you advance the focus without messing anything else up? I would never have guessed that was lit just with an LED headlamp. I’ve never had any luck except through a dissecting scope. Something always shifts and messes up the registration completely.

Created: 2012-04-04 17:25:59 PDT (-0700)
Last modified: 2012-04-04 17:50:24 PDT (-0700)
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