Diario de hsug1747

A journal entry I will be continually updating with additions to a series of observations documenting variation in blue scales of "Bluebellies", aka Western Fence Lizards.

This is another entry from a few months ago, which I am now adding to my public journal because I believe this observation requires a bit of additional explanation.

While looking for lesser brown scorpions and introduced gecko species at night in Kaanapali, I noticed some tiny, luminescent specks which would appear and rapidly fade with each wave that crashed on the shore. They were so small and scattered that I initially believed they were merely some form of visual noise (i.e. the Ganzfeld effect), however upon closer inspection, and confirmation from my younger brother that there were, in fact, transient, glowing objects appearing on the sand, I realized I was looking at some form of bioluminescence.

Up close, the specks could be seen to flash a pure neon-blue, and slowly dissipate. Eventually, we managed to collect an individual while still bright enough to detect (The organism itself was smaller than many grains of sand on the beach, and transparent) and I began to try to photograph it. I had with me the Canon EF-S 60mm 1:1 macro lens, which was sufficient to capture sand-grain sized objects in reasonable detail. I was excited to find that each speck had discernible eyes and organs, and the recognizable, Hello Kitty-like form of an ostracod. However, taking a picture of the subject proved to be more of a challenge than capturing it in the first place. Focusing at 1:1 in the dark was slightly difficult feat to begin with. The dimness of the glowing substance made it impossible to photograph at any reasonable shutter speed, even at the highest ISO and widest aperture settings, and without a tripod, any image I took either drowned out the luminescence with the flash or was nothing more than a blue smear in the darkness. In addition, each specimen lasted only a few minutes before going completely dark and fading back into the sand, adding a narrow time constraint to each attempt.

Eventually, I realized I could create an image showing both the glowing luciferin and the ostracod itself using the flash on a long-exposure shot. The photos in this observation are not "compound" images comprised of a shot taken with the flash and a long exposure, but single exposures of a 3-10 seconds for which the non-glowing parts of the image are only illuminated during the flash. This technique is effectively a normal photo and a long exposure in one, "freezing" the subject while allowing the faint glow of the luciferin adequate time to "catch up" with the light of the flash.

The non-macro shots in this observation were taken with the long-exposure feature on an iPhone 12 mini. I typically do not like the way images are processed on recent iPhone models, as it generates wildly inaccurate color and detail in an attempt to replicate the vibrance and subtlety of a higher quality camera (I have no issue with using smartphone cameras for iNat, my iPhone SE worked great for years of observations, I only have a problem with the blatant overcompensation of the newer iPhone software. I could write a whole journal post complaining about Apple's design philosophy when it comes to cameras, but I digress). However, in this case the automatic post-processing was quite useful, and represented the glowing ostracods much better at a distance than my DSLR could, at least without a tripod to take very long exposures. That said, please note that the ostracods appear FAR brighter in these photos than in real life-- the software seemed to designate them some kind of significance (maybe an algorithm intended for photos of starry skies?), and made them more prominent.

After downloading my photos, I did a bit of research into bioluminescent ostracods in hopes of refining my ID. However, I found very little info on their presence in Hawaii, with the majority of studies and sightings being in the Caribbean, Japan, and sometimes the west coast of North America.

In this post I will describe my current method for focus stacking, which can be achieved entirely on a smartphone. I have found this method to work decently well, although I will likely improve on it in the future. Any input on how to improve this process (better free programs, other techniques you've discovered, or problems with my current method) would be appreciated. I would also like to suggest setting adblockers to turn off for Focus Stacking Online-- the creators certainly deserve their ad revenue.

For the past few weeks, I have been playing around with focus stacking for ultra-macro photography with the Laowa 25mm 2.5-5x lens. While I initially sought only to find a decent, free alternative to paid programs for use on my laptop, I soon realized that I could quite easily add the constraint of mobile compatibility for the workflow I develop. This would be beneficial for field work/iNatting, since stacks can be created on the go alongside the iNat app, rather than after your opportunity to shoot another bracket has passed.

As of now, my process involves three programs:
PS express mobile app (free version)
Focus stacking online
Lightroom mobile app (free version)

Focus Stacking Online is at the core of my current method. I find that it works impressively well for a free online program, but it has a few weak points. These can be mitigated using PS express both before and after processing in FSO. Lightroom is supplemental to PS express for post-stack processing.

It should be noted that photos on iNaturalist are scientific documentation, and thus should not be altered for the purpose of being more visually appealing. This risks obscuring or misrepresenting aspects of the subject. The usage of editing I will describe in this post is entirely to preserve the genuine appearance of the subject--compensation for either a misaligned bracket, or for the free FSO software's shortcomings. Any processing, including focus stacking itself, should be disclosed in the notes of an observation. The "focus stacking" field should be applied when focus stacking is used. Including some unedited shots, perhaps at a lower magnification ratio, is also advisable, especially when an image is heavily altered.

Shooting:
To begin, I shoot a bracket (typically of 2-8 photos) using the continuous shooting mode on my camera. This can take a few attempts to get right, especially with extremely shallow depth of field (typically around 0.1mm in my case). I usually get the best results by bracing my left hand against a surface, pressing the shutter button, and gently increasing pressure from my right hand while allowing my left to give slightly. I have found that this is the most reliable way to smoothly shift the focus forwards and backwards without a tripod or focusing rail. I make sure there is at least one photo covering every area I intend to be in focus to avoid "focus gaps", which result in blurry bands on the final image.

Using, and "Hacking", Focus Stacking Online:
After achieving a satisfactory bracket, I download the images, import them into FSO (add>photo library), click "stack", and wait for the program to finish processing. This can take a few minutes. Simply importing and stacking often produces satisfactory images, particularly of subjects which have few or no long extremities, such as a a seashell, leaf, caterpillar or ladybug (at least when viewed from above). However, subjects with long legs, spines or antennae can "confuse" the program, especially if these extremities intersect. This is because slight shifts in perspective can produce significant compositional changes between shots, which result in a bracket that cannot be aligned properly. When this happens, parts of the image can become "doubled" or "broken", or the program may fail to stack the images entirely. This is a major issue for handheld stacking, as slight perspective shifts are unavoidable. Sometimes, these issues can be remedied by switching to the "beta" alignment method, selecting a new reference image, or by removing photos which cover the same area of focus as another. However, when all else fails, PS express can be used to eliminate these doubling and breaking effects.

Take, for example, this portrait of a woodlouse spider (The large image is a stack including the bottom three constituent photos):

This is the best I could get by only changing the reference, stacking method, and number of photos within FSO. As you can see, there are significant "ghostly" doubling artifacts produced by misalignment in the chelicerae and pedipalps. To fix this, I used the heal tool in PS express to simply eliminate the problematic areas on the constituent photos in which they were not in focus prior to stacking:

Detail comparison on the problem areas:

This produces a far better result, free from the issues in the first attempt. This method is ideal, because the usable part of the image has been in no way altered-- it simply eliminates the opportunity for "confusing" FSO. However, it may not always work, in which case the heal tool may also be used on an already stacked image to manually erase the artifacts. This is also useful for removing sensor dust, which is often doubled by the stacking process. If you're like me and tend to change lenses in less than sterile environments, you'll notice this issue immediately, and find that healing sensor dust on backgrounds becomes the most commonly needed retouch.

I use PS express mainly because it has the best free heal tool (may also be referred to as "blemish removal" in other programs) of any mobile app I've tried. PS express also has a substantial adjustment section, however having an additional program such as Lightroom is helpful for this stage. Adjusting exposure, contrast etc may be necessary to restore accuracy after processing the stack (stacked photos may come out slightly different from the originals), but this stage should be minimal and can often be skipped altogether.

Below are some examples of photos I have taken using FSO and the techniques described here.

All equipment I use for iNat. This is a post which I will be continually updating.

iPhone camera:
before December 2021: iPhone SE
after December 2021: iPhone 12 mini
DSLR: Canon Rebel T7 after September 2022
DSLR: Canon 6D after February 2024
Flash: built in flash or Godox TT600, sometime connected with Meyin hot shoe connector cable February 2024
Focusing/underwater light: Suptig Diving Light (LED attachment designed for Gopro) after February 2024
Lenses:
-Macro: Canon EF-S Macro 60mm F/2.8 (September 2022 onward), Laowa 15mm f/4 Wide Angle Macro (September 2023 onward), Laowa 25mm f/2.8 2.5-5X Ultra Macro (December 2023 onward), Laowa 60mm 2x (April 2024 onward)
Many macro observations use multiple lenses.
Telephoto: Canon 75-300mm telephoto
other: EF-S 18-55 zoom (kit lens which I rarely sure)
Backpack: Altura Photo Camera Sling Backpack
Extension tubes: cheap set from amazon
Diffuser: this , but I don't use it on many observations
after march 2024: homemade diffuser hood
Underwater: FUJIFILM FinePix XP140 (some older obs with XP80), or the DSLR in Tteoobl waterproof case bag
Some old observations (2015 and earlier): Nikon Coolpix s6200
infrared:
-Fotasy variable IR filter, camera specified per observation. (I cannot recommend this filter-- it does not work at any setting other than 750nm, and lets through too much visible light for use with either of my unmodified DSLRs, effectively just red ND filter. It also produces dark bands sometimes.)
-trailcam

Audio recordings are taken on my phone for now.

Various stuff I may wear while hiking or carry with me:
-small jar
-tweezers
-plastic ruler broken in half to fit in pocket
-coast g20 "inspection beam penlight" (little flashlight)
-Vansky black light (for scorpions)
-hair ties/beanie hat (keeps hair from getting in my face, which is annoying when taking pictures. Brim hats bonk the on camera flash)
-plastic critter keeper with plexiglass rectangle (used to place fish in for photos, like one of these )

software/online tools:
extension tube calculator: https://thingsupclose.com/tools/extension-tube-magnification-calculator/
PS express mobile app (free version)
Focus stacking online
Lightroom mobile app (free version)
gimp occasionally maybe

Menenerus bivittatus with offspring. Multiple small groupings of M. bivittatus were present under peeling bark flakes on western sycamore, this one included a single adult, around 8 juveniles, and one Sassacus vitis. Focus stacked images.

Two sawfingers and one female swollenstinger, pretty good for January. Likely displaced by rain, as it's a little early for them to be out of their own accord. Also the first time I've gotten satisfactory results out of the technique described in this journal post on a scorpion.