Focus Stacking: An Introduction

March 6th, 2017 (trackback)
Belionota sumptuosa (Indonesia)

At left is a photo of a Belionota sumptuosa from Indonesia. Commonly known as a Tricolor Metallic Wood-boring Beetle.

It isn’t a regular photo, though. It is a focus stacked image.

Specifically, it is 276 photos combined to make a single image. When shooting macro, the depth of field — the distance in front of the lens that is in focus — tends to be really narrow. By taking a bunch of photos where each has a different depth in focus and then combining only the in focus areas from each image, one can effectively create a composite image that is entirely in focus.

So, this is really 276 images taken across about 40mm of camera travel; about 0.15mm of travel between each picture taken. I’ll cover that in a later post

Since optics are optics and physics are physics, changing the focal plane by either moving the camera ever so slightly (10 to 20 microns per photo, in this case) or by changing the focus depth via the lens’ focus ring, the scale of the subject changes just slightly and anything in the foreground becomes blurry and obscures the background.

All that has to be compensated for and there are a handful of software stacks that do exactly that. I’ll discuss those in a later post.

Belionota sumptuosa (Indonesia) Source Image

To put it into perspective, this is a single frame in the stack.

Only the tip of the feet and antenna are in focus. The focal plane is so shallow that not even the leg is in focus and the rest of the bug is entirely blurry.

On a lark, I put together a video of all of the frames in the stack followed by the final image. In 4K.


There is nothing about focus stacking that requires a bit of computer controlled technology to move the camera multiple microns per image with crazy studio lighting (all of which will be discussed in later posts).

In fact, focus stacking really only relies that you can hold the camera still enough between multiple photos while also changing the focal plane, either by moving the camera or adjusting the focus ring.

For example, the image at left is a bit of gooey fungus growing in a fairly dark part of the forest. Normally, such a shot would require a lot of flash, a really tight aperture (high number– backwards), and as slow of shutter speed as possible. In a single shot, there would likely be some bright flash highlights, too.

In this case, I braced the camera on a log, cranked the aperture to relatively wide open so I could have a reasonably low noise (low ISO) image while still having a handheld compatible shutter speed and then shot 11 frames while varying the focus depth via the lens’ focus ring. I did use a flash, but I was able to turn down the intensity a lot, yielding fewer highlights.

So, yes, handheld focus stacking is possible. But hard. Add a cheap, small, tripod and it is no longer hard. Add a focus rail and the options expand. Etc until your wallet is empty, as usual.

(From Ann) Mary Jean Heyssel Bumgarner — 4/2/26 – 12/11/16

February 8th, 2017 (trackback)
Blystone Kids with Grandma/Grandpa

Mary Jean Heyssel Bumgarner

4/2/26 – 12/11/16

Our beloved wife, mom, mom-in-law, grandmother, great-grandmother-to-be, sis, sis-in-law, aunt, cousin, best friend, friend, mentor, muse and all around wonderful human being slipped out of her place here on earth and into the great unknown last night at 8:12pm, surrounded by her beloved Roger (our dad), her 3 children and other fambly members. It was peaceful and good.
She lived and loved fully and well and taught many lessons during her life, though we didn’t and she didn’t know she was doing that…and we’re all the better for it.

Surrounded by love she was, as we always were and are – from her.

Such a good, wonderful, love-filled 90 years she had on this earth!

(Gotta believe mom and Rem are kickin’ it up together!)

(From Carrie) RIP Mary Heyssel Bumgarner (4-2-1926 — 12-11-2016)

January 3rd, 2017 (trackback)

This is my sister Carrie Bumgarner’s thoughts on the passing of our mother, Mary Bumgarner. She originally posted this to FaceBook and asked me to capture it here so it may last.

The photo is of Mom & Dad from, if I remember correctly, 1952. It was taken in California as they journeyed West prior to going to the Far East for Dad’s stint in the MASH 8063rd in Korea.

Mary & Roger Bumgarner in California

As many of you may know from the wonderful tributes by my sister and brother posted earlier, my dear mother, Mary Heyssel Bumgarner, passed away on Sunday. While I could add to the tributes, what I really want to say is thank you. She gave us an invaluable gift at the end. She “knew” she would not last until Christmas so she called us calmly and told us to come home. We did and her whole family was with her for Thanksgiving. She gave us the time to say “I love you,” “Thank you” and “Goodbye.” We laughed, we cried, we reminisced, we read poetry, and we philosophized. We actually got to know each other better. She gave us invaluable quality time. It made it both easier and harder to let her go.

A true force has left this earth but not our hearts or our minds. I leave you with one of her and her mother’s favorite poems:

There is a destiny that makes us brothers

None goes his way alone

All that we send into the lives of others

Comes back into our own

I care not his temples or his creeds

One thing hold firm and fast

That into his fateful heap of days and deeds

The soul of man is cast.

Thank you mom, I will miss you and love you forever.

On Death And Taxes; Some Tools to Make End-Of-Life Easier

December 25th, 2016 (trackback)

We all face the death of our family’s older generation at some point or another. Death is inevitable.

Here are some thoughts and tools that I have found to be very helpful.

There are the obvious; make sure there is a will in place. Make sure the household can be maintained upon death; bills paid, taxes paid, bank accounts accessed without probate, etc…

Then there is the non-obvious. Or, at least, tools I never saw mentioned as we approached Mom’s expiration date and prepare ourselves for our father’s eventual death.

More likely than not, the older generation will have cabinet(s) full of paper records. Everything from real estate transactions to legal agreements to personal letters to certificates, etc….

While preserving the original of some of these documents is critical, having easy access to all of the documents while also preserving them is also critical.

To that end, get a good document scanner. The Fujitsu ScanSnap iX500, in particular. Fujitsu also makes a cheaper, portable, variant that works well, but is not nearly as bulk-friendly as the ix500.

It is the best document scanner I’ve used (and it does a good job on photos, too). The software — no surprise — is kinda lacking in the UI department, but that’s OK. You don’t want to have to interact with any UI at all and it can easily be configured to do exactly that.

Specifically, you want a solution that enables very quick scanning of hundreds or thousands of pages with minimal interruption. And the ScanSnap does exactly that. Stick a document in it, push the blue button, done. It’ll detect if there is a jam of any sort, but does a remarkable job of not jamming. It will OCR the documents as they are scanned, meaning that they are indexed by SpotLight for easy searches later (this has been invaluable for cross-referencing documents).

I configured the iX500 to scan straight to an iCloud folder. Once captured, I’ve then been renaming and creating a folder structure, as warranted. Being in iCloud, I have easy access to the documents from any of my devices. I do wish that iCloud allowed folders to be shared amongst users (radar filed), though.

In our family, my father was (he hasn’t picked up a camera in a couple of decades) an avid photographer. As such, we have boxes and boxes of slides dating back to the 1950s. Beyond some genuinely amazing bits of family history, said slides also capture little bits of history — and sometimes big bits — that are of interest well beyond the family.

Now, I could send these slides off to a service like iMemories or the like and have them scanned. And I might still do that. But it is scary to think of the only copy of said slides being out of our hands even for that.

For the 1200 or so slides my Dad had, I picked up a Wolverine F2D 20MP slide scanner. Key features are that it works quickly, writes the images to an SD card that can be imported just like an SD card from a camera, and the results are of good quality.

It does all that. Quite well. And very quickly. You can get higher quality by spending more and going with a computer connected device, but it isn’t nearly as convenient.

In scanning all of the images, it also catalyzed some wonderful conversations with my father as he relived some of the memories contained within.

As it turns out, my father has one of the single largest collections of slides from a single MASH unit in Korea that I’ve been able to find. Over 200 images of his time in Korea. Once I’m done capturing them, we’re going to donate this treasure trove of documentation to one of the historical preservation groups focused on the Korean war.

8063rd MASH Sign

This is an image from the slide scanner. A slide from ’53 in Korea, specifically.

Pretty good for a slide that has been shoved away in a box in an attic or a corner of the garage in Midwest weather for 60+ years!

Beyond the aforementioned obvious, this post is really to encourage you to preserve the past. All those documents? The slides? They mean little to anyone but the family, but they surely mean a lot to the family.

And, while you still have the chance, sitting down to talk through the events of your elders is a tremendous way to learn much of your history.

RIP Mary Heyssel Bumgarner (4-2-1926 — 12-11-2016)

December 20th, 2016 (trackback)
Mary Posing

RIP Mary Hessel Bumgarner. Born April 2nd, 1926. Died December 11th, 2016.

AKA Mom.

Many have asked how Mom wanted to be honored and remembered. She had three causes that she actively supported in the past years and asked that others support them as well.

For straight donations, please support The Food Bank of Central Missouri or a like minded organization in your area. Alternatively, Mom supported The Rainbow House and encouraged others to do the same.

In more recent years, Mom was very vocal in her support of The Slow Food Movement. She asked that we encourage everyone to join.

Not just Mom to her three children, but a matriach.. a muse… an advisor… a mentor… a critic… a master chef… and many many more roles to many many people.

While I — we — will miss her and we do grieve, she would tolerate no sadness in this passing. Mortality is unavoidable and her’s was a life fully lived.
She lived a 90 year long life that can only be called extraordinary. She spent 67 of those years happily– nay, passionately– married to my father, Roger Bumgarner, a man whose compassion, strength, humility and patience is equally as extraordinary.

Beyond all the people whose lives were enriched by knowing her, she left a legacy of many stories. Stories that underscore that up until her last breath, she did it her way. And stories that we can all learn from and, in so doing, if we act upon their lessons, the world will be a better place.

Stories that ultimately center largely around a few central themes.
Be kind. Through kindness, you’ll find friends and gain knowledge in the most surprising of places.

Be curious. Everywhere you look — truly, everywhere — there is something to be learned. New science. New art. New patterns. New ideas. New ways. Open your mind and it will be enriched.

Be accepting and kind. No religion, no skin tone, no orientation, no nationality, no age, nor any other difference means automatic condemnation. Every person deserves a chance.

Embrace change as it is the nature of the world. To do otherwise, is to be left behind.

Think. Observe. Experiment. Problem solve. Debate. Argue. Embrace being wrong. Correct. Move on. Repeat. Share.

Be generous. Not just with money, but with your time. Share your knowledge and experience with others. Catalyze growth in those new to the world. Encourage their creativity and interests. Mom was a muse to many, sometimes directly and oft indirectly. Many a career was accelerated, if not made, because she provided a bit of guidance or support at a critical time.

A wonderful woman has left this world. The world, though, will reap the benefits of her presence for years to come.

A quick word on that photograph. It was taken a couple of years ago, well after her COPD diagnosis and many many months more life than anyone was led to expect (Mom did not like to be told what to do).

If you know Mom, you know that she absolutely hated having her photo taken. I was surreptitiously trying to get a decent photo a couple of years ago and she was, as is usual, giving me lens melting glares of disapproval.

Finally, she said, “I’m going to die soon and you’re going to share a photo of me with everyone. I’ll be dead, I won’t care if it is bad or not, but… here.. I’ll pose once.” Credit to Christine for teaching Mom a proper pose.

May we all live a life so full of adventure, love, beauty, and so totally on our own terms.

Miss you, Mom. So long and thanks for all the fish (and everything else).

iOS Travel Software

April 22nd, 2016 (trackback)

We just spent a couple of weeks traveling around Ecuador.   Fantastic country, you should go! (We missed the earthquake by days. Devastating. They could use our help about now.)

Of course, we had our bags of electronics.  Lighter than books and necessary for processing photos.  Entertaining, too.   And, of course, with the right software, they can vastly augment the travel experience.

The key is to find software that works well in areas of the world where Internet connectivity is a rarity.   Offline modes are key.

Here are a handful of iOS applications that have proven to be extremely valuable during our travels.    They fall into two categories;  mapping and translation.


For mapping, my use fell into two focus areas.  First, there is the obvious need to figure out where we were and what might be around us (and how to get there).  As a secondary use, being able to drop pins on a map and take a few notes about what was found at that location proved handy.

For offline maps with tons of information, I haven’t found anything better than Pocket Earth (there is a pro version that costs money up front, but appears to have unlimited downloads of the offline maps which are in app purchases in the free version).

Beyond having excellent maps, there is a $5 add-on that offers topographic maps, too. This was fantastic as we wandered through the Andes mountains. We could spot volcanoes and know how high the peak was above us or know how far a waterfall was falling. Or how deep the gorge was that we were zip lining across.

As well, Pocket Earth will download wikipedia articles for whatever regions you download and it can also download wikivoyage articles, too. These are placed on the map so you can quickly learn about wherever you are!

You can also drop pins in Pocket Earth to keep track of where you’ve been., however, has better pin dropping and diary features, and supposedly integrates with openstreetmap’s editing capabilities so you can push new points of interest back to the OSM database.


After having been to South and Central America a few times, I’m surprised by how much spanish I’ve started to understand and, even, speak. But I’m so far from being able to claim knowledge of said language that I need help. Lots of help.

This is where the Star Trek sort of experience kicks in; years ago there was Word Lens which did real time translation of text by simply pointing your iPhone’s camera at said text. Works great. Still does, but it is now in Google’s Translate app.

That is about all Translate does offline. The iOS app can’t do offline dictionary based translation, doesn’t have phrases, etc…

However, Xung Lee has got this covered exceptionally well. Traveling with this app bundle — Spanish English Dict Box Pro and Translator Pro Offline Spanish English Sentences — was fantastic. We were able to consistently convey what we needed in a polite (we checked with our bilingual guide to make sure we were conveying politeness and appreciation for the patience of whomever we were interacting with) fashion!

The dictionary app provides more than just translations of words, but every word comes with a long list of common combinations. Looking up “water” reveals “boiling water”, “carbonated water”, “cold water”, “hot water”, “foul water”, “ice water”, etc.. etc… etc…

The translator pro app is focused on phrases and sentences. Look up “tea” and you get all kinds of phrases about asking for tea, the cost of tea, someone making tea, etc…

Combine words and the app will come up with common phrases that involve both words. “Cold beer” comes up with phrases about desiring a cold beer and phrases about how nice a cold beer is on a hot day.

My kind of apps.

All in all? Probably $12 to $15 in apps. Which, frankly, is ridiculously cheap given just how much the above augmented our travel experiences!

Highly recommended.

Review; Brinno TLC200 Pro Time Lapse Camera

June 25th, 2015 (trackback)

One nice fallout from the smartphone revolution is that cheap embedded controllers, camera sensors, and flash memory has dropped in price while the capabilities have jumped by leaps and bounds.

Unfortunately, the quality of the user experience has not seen the same revolution.

After having played with time-lapse photography on my iPhone, I concluded that there was much more to explore, but I would ideally want a dedicated camera that I could set, forget, and still be able to use my iPhone or iPad for something else.

Searching around revealed that the Brinno TLC 200 Pro is the best timelapse camera currently available.

The Brinno is a small, dedicated, timelapse (or still frame animation with external trigger) 720p camera that supports interchangeable lenses (and there is a microscope attachment. Brinno also makes a waterproof case that both fits perfectly and can be mounted to a tripod.

The camera has a slew of your typical manual controls; white balance, shutter speed, HDR levels, etc… but the adjustments are hidden in a maze of menus and the three buttons used to navigate make for a shoddy user experience. Livable, but shoddy.

Fortunately, once the camera is configured, you can basically bang on the big OK button to start recording. The built in LCD allows you to align the camera, but does not support playing back captured content.

The Brinno writes videos in the AVI format. Makes sense; AVI can be as simple as a file with a sequence of JPG stills. Unfortunately, neither iOS nor OS X will decode AVI directly. I use Smart Converter Pro 2 to convert the videos. The free version works, but doesn’t give you quite as much control over the process and is strictly one video at a time (the Brinno splits movies at 4GB, so there is often multiple movies to convert).

You can control the frame rate of playback. This, combined with the ability to set the duration to wait between shots taken means that, with Brine’s handy calculator, you can easily create a time-lapse for any length of time (and the Brinno has a “timer” feature that will cause the camera to turn on only during preset blocks of time.)

Ultimately, I find it is preferable to leave the Brinno in ASAP mode; it takes a new shot as soon as the current shot is done (i.e. if the shutter speed is 8 seconds, then you get one shot every 8 seconds). I then compress time however much I desire using Final Cut Pro.

Fun device. Beyond clouds and sunrise/sunsets, I will be capturing all kinds of chemical and physical processes that are then brought from a glacial pace to human speed.



At left is the Brinno in its waterproof case sitting on a Gorilla Pod to record a timelapse of the reflections on the pond. You can see the all too small display and the rather poor two 3 button UI.

While the UI is bad, the camera’s battery life is good to excellent (it can last many months when shooting a frame every hour or more). The video quality is mostly quite good, but suffers from low light noise and the exposure tends to bump down in lock step as the amount of light increases, leading to sudden changes in light level in videos of sunrises and sunsets.

Even with the criticism, I can still recommend the device if you either need to compress time when recording video or simply want to play with different time scales. It is really a lot of fun to set it up and then see what 5 hours (or days? months? The Brinno can do it) of the world looks like compressed into a couple of minutes!

KitchenAid Compatible All Stainless Steel Meat Grinder / Food Chopper

March 3rd, 2015 (trackback)

Unfortunately, our 20+ year old KitchenAid mixer was lost in the fire. Of course, it had to be replaced because such a mixer is a staple in any kitchen. After doing a ton of research, it was both confirmed that KitchenAid continues to be of excellent make and that one should really go with at least the 6 qt model as it has a significantly more powerful motor than the 5 qt motor.

Yes, we went with the Candy Apple Red model. It looks quite stunning on the black granite and against the blue tile backdrop of our remodeled kitchen.

Beyond mixing dough, the KA mixers can drive a whole series of attachments. Frankly, it works the same way as a John Deere tractor. There is a little port into which you plug various attachments and the high torque motor then drives said attachment. This includes everything from ice cream makers to grain mills to juicers to pasta makers to, yes, meat grinders.

Oddly, the KitchenAid meat grinder is largely made of plastic. It doesn’t have anywhere near the same build quality as the rest of the mixer.

Quite a bit of searching turned up Smokehouse Chef’s very well reviewed Stainless Steel, Dishwasher Safe, Meat Grinder / Sausage stuffer / Food Chopper. It is worth every penny of the price. It features a rock solid all metal build, a much much larger food hopper than the KA grinder and quite a few more cutting discs. I haven’t tried the sausage stuffer, but it seems quite high quality, too.

Quite a significant upgrade. It’ll work with all models of KA mixers, but they recommend — and my experience confirms — that it really works best with the higher wattage motors.

Note: Instead of a tilt head, this model has a lifter that lifts the bowl while the head is fixed. While the mixer is larger capacity, it requires less vertical space than the 5 qt model.

Read the rest of this entry »

PhotoSweeper: Photo De-Duplicator for Aperture / iPhoto / Lightroom / etc.

January 20th, 2015 (trackback)

Since I started taking photos 15 years ago, I’ve amassed a pile of images. 25,000 or so photos sourced from various cameras, phones and a handful that were scanned and imported. They have been managed manually, in various flavors of iPhoto, the occasional random application, and — for the past few years — in Aperture. Copies of the photos have lived on various computers and, even, have been recovered from backups after a rare hard drive death (multi-point backup strategy FTW!).

End result?

25,000 images of which somewhere between 5% and 20% are duplicates. Many of them are straight up duplicates; copies of the same image with different filenames resulting from merging various libraries or importing source media to multiple destinations that were later merged. Some are more insidious. Somewhere, something decided to down-res a slew of images and re-import them. Somewhere else, something decided to re-encode all my JPEG images (before RAW) at the same resolution, but with much higher compression.

Slogging through all those images would take hours. Days, really, as it’d have to be done in my spare time. And, given that it is a task I’ve been avoiding — digging the whole deeper — for a decade+, clearly not going to happen soon.

Clearly, there has to be a better way. And there is!

A quick search yielded PhotoSweeper.

On first pass, it quickly eliminated all straight up duplicates where the actual contents were identical. This took less than ten minutes to do on those 25,000 images and it eliminated nearly 4,000 dupes (and triplets and the occasional quad).

The second pass is where this software really shines. I configured it to do a content comparison and flag any sets of images that were pretty close, but not necessarily exactly, similar. In this case, I used the “approximate, align and blur” method. That is, PhotoSweeper re-renders each image as a 144×144 grid of pixels, then blurs it slightly, and aligns the edges. The resulting icon-ized images are compared and any that are similar enough are flagged as potential dupes. It is then a matter of review-and-compare. The arrow keys are used to navigate and the return key to toggle whether or not the image will be trashed.

One click and all the identified dupes are dumped in the trash.

What would have taken days of tedium was reduced to less than an hour. Personally? I would have paid $50 — nay, $100 — for this and have considered it a bargain. It saved me that much time (frankly, it finished a task in short order I’ve been putting off for a decade) and now my remaining organization task is largely one of actually looking at, tagging, and categorizing the photos.

And sharing them with my family. Because that’s what it is all about (for me).


January 6th, 2015 (trackback)
Grizzly bear (Ursus arctos horribilis)

Over the summer, we escaped for a while to Alaska via a trip put together by International Expeditions. This was our second trip with the company — our first being a week on the Amazon River (fun story, photo set on flickr) — and it certainly won’t be our last as International Expeditions does a fantastic job.

For the Alaska trip, we opted for the 11 day grand tour.

Beyond a fantastic tour of glaciers, a backcountry lake lodge, and Denali National Park, highlights included fantastic lodging in the most remote of places, incredible homemade meals, mind blowing scenery, and a wonderfully friendly group of random travel companions that quickly become a temporary family (with whom we wouldn’t mind crossing paths again!).

It was, no surprise, a great place to take photos and I’ve pushed an album to Flickr.

Alaska is both surprisingly diverse and, yet, equally as surprisingly limited in natural diversity.

On our tour, we ranged from a coastal rainforest to arctic tundra and even spent some time in the air flying around Mt. Denali.

And that covered a very tiny part of the state. It is also hard to fathom just how big Alaska truly is. Watching this glacier calve, we were nearly 1 mile away from it and yet it still seems to tower above us and there were still miles of glacier behind and above it! And beyond the top of that glacier? An ice field that is larger than most states in the lower 48.

Alaska is very different than anywhere else we’ve visited. Whereas the Amazon was full of a seeming infinite number of species of plant an animal, there are actually very few species in Alaska; only 150 or so native plants have been cataloged (with many variants within those particular individuals).

While in the rainforests of the equator, things rot with incredible speed, trees may lie on the ground in the Alaska rainforest for years because their simply isn’t the warmth or sunlit energy to support the decomposing agents. Thus, the Alaskan rainforest floor is a thick layer of, well, mulch on top of rock. Springy, almost magical to walk on. But no real dirt.

And some of the seemingly most innocuous and beautiful plants are quite deadly.

Even the mosquitos are different. In Alaska, the mosquitos are the top pollinator. All those incredibly yummy tundra blueberries, cranberries, and crowberries? Pollinated by mosquitos. Still annoying critters. But mosquito defense did lead to some interesting fashion statements.

A fantastic place to visit!