05 de abril de 2024

On uploading cats

Recently, I have been uploading photos from a trailcam to iNaturalist. This has posed the question of whether or not I should upload the domestic cats that pass by it. Typically, I do not upload animals which are presumably pets or livestock, since non-wild animals aren't really what iNat is "for", and because they belong to someone else. However, I have decided that it is useful and appropriate to upload cats, mainly for two reasons:
1) because many are uncollared and potentially feral, and
2) because outdoor cats have a very significant ecological impact, and are therefore of value as "wildlife" data even if they may be pets.

That said, I would take photos down if the cats' owners contact me requesting I to do so.

Publicado el abril 5, 2024 04:54 MAÑANA por hsug1747 hsug1747 | 0 comentarios | Deja un comentario

04 de abril de 2024

Post-Flood Pupfish at Death Valley: accessibility, and my notes on the salt creek population

This journal post dedicated to my recent experiences visiting the habitats of two rare pupfish species (The Salt Creek Pupfish, Cyprinodon salinus ssp. salinus, and Ash Meadows Amargosa Pupfish, Cyprinodon nevadensis ssp. mionectes) will cover two topics: One, the accessibility and condition of three localities, and two, my notes and observations at the Salt Creek population. I hope to address the current scarcity of up-to-date info on these locations, and expand upon my posted observations regarding the unique and transient state of salt creek both as a habitat and as a tourist attraction.

After the destruction of the Salt Creek Interpretive Trail (boardwalk) by seasonal flooding, accessing rare pupfish habitat is no longer as straightforward as driving a few minutes from Stovepipe Wells. Over the past few days camping at Furnace Creek, I visited three pupfish localities (two of the Ash Meadows Amargosa Pupfish, and one of the Salt Creek Pupfish): Crystal Springs, Point of Rocks, and Salt Creek. Eventually, I hope to add another journal post regarding the Devil's Hole, Saratoga Springs, and Cottonball marsh pupfishes, as these locations were out of the scope of my recent trip.

The now-destroyed Salt Creek Interpretive Trail will be referred to as the SCIT for the sake of brevity.

Crystal Springs (Cyprinodon nevadensis ssp. mionectes):
This is likely the most obvious post-SCIT pupfish viewing location, across the CA-NV border and some 45 minutes away from Furnace Creek. The boardwalk loop is connected to the ash meadows visitor center, which is a good resource for information on the area's many endemic species. At the time of my visit, the attraction was not excessively crowded. However, this location has two main issues for discerning amateur naturalists hoping to watch or photograph pupfish. The first is that the boardwalk does not allow visitors to get nearly as close to the water as the SCIT once did, requiring the use of binoculars/telephoto lenses to get a detailed look at the best sections of the pupfish population. The main pool at Crystal Springs is beautiful, and densely populated with C. nevadensis mionectes, however the distance significantly restricted photography. The other issue with this spot was the dominance of invasive sailfin mollies-- side from the main pool, Crystal Springs is home to far more mollies than pupfish.

Point of Rocks (Cyprinodon nevadensis ssp. mionectes):
Also within Ash Meadows, Point of Rocks consists of a mixed boardwalk/dirt trail directly accessible from a parking lot and small picnic area. The central attraction of the location is Kings pool, a clear blue pond similar to Crystal Springs' main pool. However, Point of Rocks differs in that the dirt trail comes into direct contact with the edge of the pool for a short section, allowing for close up viewing and photography of the pupfish without disturbing the habitat. I spent a significant amount of time kneeling by the water's edge, and was greatly satisfied with the photos I could get with a macro lens from just above the water. In addition, I did not see sailfin mollies at Point of Rocks. There were a few introduced mosquitofish, however the Ash Meadows Amargosa Pupfish is very clearly the dominant species. Point of Rocks was not excessively crowded at the time of my visit, but did seem fairly popular.

Salt Creek (Cyprinodon salinus ssp. salinus)
Salt creek is located at the end of a currently unmarked 2.5 mile sandy road not far from stovepipe wells. This road is closed, however, according to attendants I talked to at the furnace creek visitor center, the road and creek are open to foot or bike travel. I opted to ride a bike to the creek, which may be more difficult than walking depending on the type of bike used. A mountain bike or fat-tire sand bike would be ideal, although I found that about 80% of the distance was bikeable with decently robust regular tires, as long as I rode on the rocky ground alongside the rode rather than the sandy road itself. Including short water breaks, the ride only took about 10-15 mins. On the way there, I encountered a few people exiting the area on foot, however while I was at Salt Creek I saw zero visitors. The boardwalk, parking lot and bathroom are reduced to ruins; only a few informational signs are left standing. In contrast, the creek is fast-flowing and teeming with pupfish. The area can be explored for as far as one would like to hike.

The single issue with salt creek is the presence of large, incredibly persistent horseflies (Tabanus punctifer). I was constantly bitten by these flies while photographing the pupfish, sometimes even bleeding through my shirt. I would strongly recommend wearing thicker clothing if anyone plans to visit the location, as they are more than capable of biting through fabric. Prospective visitors will likely be the only available human host(s) for a radius of multiple miles, and, like myself, find themselves constantly swatting at the prick of the flies' scalpel-like mouthparts.

Since there were no other visitors while I was at the location, I was able to observe the pupfish fully undisrupted. The creek was much wider, and more washed out than I had seen in 2018, with numerous branches and islands forming a flat expanse of sandy wetland. Aside from the fish, and clumps of algae along the edges, there is nearly no other life in the creek itself, although it is flanked by the occasional creosote or other desert bush. I did not observe any of the once-ubiquitous pickleweed (Allenrolfea occidentalis), nor the abundant aquatic insects of locations such as badwater. However, I did observe an impressively large Hogna wolf spider at the edge of the creek, which, in my brief experience, seems to be a species associated with high-salinity springs, or water generally, in Death Valley. The pupfish themselves seemed to be thriving-- large schools moved up and down channels of the creek, individuals could be seen scrapping in signature puppylike fashion. I often observed the fish feeding on algae at the edges of the creek, at times with their bodies mostly above water in order to access it.

The most fascinating behavior I witnessed at salt creek was the pupfishes' apparent affinity for isolated pools connected to the main creek only by narrow, winding corridors seven or so feet in length. These channels are barely wide enough for an adult pupfish, and in some sections only milimeters deep, forcing pupfish to wriggle through the sand rather than swim. Despite this, the channels saw much active use, with adult and juvenile pupfish traveling in both directions. Interestingly, the adult population of the pool I observed most closely (the one pictured in my observations of the channels) seemed to be majority female. Since there did not seem to be any increase in accessibility to food at the pool, its usage may be as a sort of sanctuary from the constant aggression and territorial behavior present in the running sections of the creek, insured by the greatly reduced adult male population. However, salt creek's ecology is unique and complex, and there may be other reasons to travel to these pools, perhaps differences in water chemistry/salinity or temperature, which I did not have the instruments to measure.

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An adult female pupfish traveling through the channel.

The presence of these "highways" highlights the fragility of the salt creek pupfishes' habitat. While in its current state, the creek receives little traffic from visitors, it would only take a single misplaced footstep to trap schools of pupfish in detached pools. I fear that, in absence of a project to install a new boardwalk to contain foot traffic, reopening salt creek as a tourist attraction could be disastrous for the structure of the salt creek habitat. That said, the pupfish are an incredibly resilient and adaptable species, and I do believe that visiting the creek without the restriction of the SCIT is an incredible opportunity for amateur naturalists to observe and photograph this incredibly rare species freely, so long as great care is taken not to disturb their environment.

Attached are all of my observations at and around the mentioned locations on this recent trip.

Publicado el abril 4, 2024 07:23 TARDE por hsug1747 hsug1747 | 31 observaciones | 1 comentario | Deja un comentario

16 de febrero de 2024

Laowa lens comparison

Observations listed are of the same group of Narnia femorata. First observation was shot using the Laowa 25mm at 2.5x magnification on APS-C (Rebel T7). The second observation contains images taken with the Laowa 15mm wide angle macro, on full frame (Canon 6D) and the Rebel. The third pic is at about 7x magnification, using extension tubes in conjunction with the Laowa 25mm on full frame. All are single shots.

Publicado el febrero 16, 2024 09:37 TARDE por hsug1747 hsug1747 | 3 observaciones | 0 comentarios | Deja un comentario

04 de febrero de 2024

Rotifers

Rotifers collected by agitating algae in a birdbath with a toothbrush.
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Publicado el febrero 4, 2024 09:11 MAÑANA por hsug1747 hsug1747 | 2 observaciones | 0 comentarios | Deja un comentario

29 de enero de 2024

First scorpions of 2024

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.

Publicado el enero 29, 2024 07:13 MAÑANA por hsug1747 hsug1747 | 2 observaciones | 0 comentarios | Deja un comentario

25 de enero de 2024

Jumping Spider with Offspring

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. AF186864-AF56-4-B68-B9-D0-19972-D0-F5-DDA

Publicado el enero 25, 2024 08:59 TARDE por hsug1747 hsug1747 | 2 observaciones | 0 comentarios | Deja un comentario

21 de enero de 2024

Equipment

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).
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

Publicado el enero 21, 2024 05:29 MAÑANA por hsug1747 hsug1747 | 1 observación | 0 comentarios | Deja un comentario

Focus Stacking in The Field Using Free Programs on Mobile

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):

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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:

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Detail comparison on the problem areas:

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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.

Publicado el enero 21, 2024 04:22 MAÑANA por hsug1747 hsug1747 | 21 observaciones | 0 comentarios | Deja un comentario

14 de enero de 2024

Hawaiian Umihotaru ("Sea Fireflies")

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.

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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.

Publicado el enero 14, 2024 08:41 TARDE por hsug1747 hsug1747 | 1 observación | 0 comentarios | Deja un comentario

13 de enero de 2024

Bluebellies

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.

Publicado el enero 13, 2024 07:10 TARDE por hsug1747 hsug1747 | 10 observaciones | 0 comentarios | Deja un comentario