All posts by Biolapse

Biolapse History part 2

Moving on to Moss
November 2013


There is certainly something wrong with my controller, it is some sort of a wiring problem but honestly im not too worried about it. I just run the output to the Chronocontroller, then out again to the camera. So the CC sits in between and this seems to settle things down a bit.

I plan to build a far more robust controller in the near future, so this is an acceptable solution.

I have moved onto new things! Live Moss! and encountered new problems, with Flicker.

The clip at the of this post was shot at f/3.2, ISO 200, 1/80s, with an ND filter.2 strobes are being used.

I know the flicker is not from aperture inconsistencies, as the lens is native f/2.8 and i have shot timelapse at f/3.2 on a regular basis and never had a shred of flicker.

clips i have done in the studio in the past normally look better than this, i think the most likely culprit at this point is the elinchrom strobes. Maybe the flash tube is getting tired, or maybe at slower shutter speeds such as 1/80 it shows more variation in the discharge of the flash. I might try bumping it up to 1/125th and see if that helps.

Either way i am pretty excited about the following clip, it is finally starting to get in the direction I am hoping to go.

Not too shabby huh? maybe a good deflicker program could help.

Towards the end the moss really starts to breathe!

SO I have been monitoring the temperature and humidity in the room, and normally it sits around 30-40% humidity which is pretty high for Colorado, but still pretty low for a lot of the plants i am hoping to grow in the future.

I stuck a humidifier in the room and got it up to 80%, but I do not know if a general room humidity level of 80% is a good idea, ill have to do some reading. I don’t want to get any mold growing in the room. I think i want to try a more localized “humid zone” right around the plants by blasting them with fog between shots.

I have not seen any off the shelf humidifers that really will be able to do what I am wanting, they already have the controls built in, limited reservoirs, and counter productive form factors to what I am trying to do.

So i guess ill just have to build my own damn humidifier. Parts have been ordered, I’m hoping to have it up and running this weekend. I was suprised with how inexpensive the parts are, with the savings I was able to pick up a large plastic enclosure i can use for the next incarnation of GreenThumb where I can have the switched outlets on the side of the box. Im pretty excited to get started.

Flicker is getting worse
December 2013

So I think the problem here is the strobes I am using.

The while the Olympus OMD is no Nikon D4, I’ts no cheap point and shoot either. I have managed to get some excellent time lapses with it and it is not in any way prone to flicker.

But it is getting worse. Shooting wide open, fast or short shutter speeds, I think the problem is the strobe is getting tired.

I tried using LRTimelapse, but I don’t know about my workflow just yet. I have never had to deal with flicker, so this is a bit of a learning curve for me

here is a clip. The first part shows it with no deflickering. Second shows it with deflickering with a wide reference point across the middle of the image, and the last shows it with the reference point on the rock. The final shows all 3 sequences lined up to see the results of this.

I am open to comments and reccommendations, as well with workflow suggestions.

My workflow is as follows

1) shoot everything RAW

2) Bring images into ACR, make any corrections/adjustments and crop, save as Jpeg at highest resolution.

3) Bring images into Adobe Pre-Pro, put in a sequence 1 frame per image, and scale to frame size.

4) Export.

now I don’t go crazy with 4k and stuff, maybe when I get better at this and further along in my project i will start working for 4k, but for now this is just really test and demo stuff.

With the deflickering i loaded everything in LRTimelapse after step 2, modified the existing exif with the JPEGS, then saved new Jpegs. (in this case I wanted a no-deflicker and deflicker attempt to see the difference)

I really do think the problem is the Strobes. I have another lighting solution i plan to start working on as soon as time allows which will use high intensity LEDs instead of flash bulbs. I suspect I should get a very even and consistent light output.

Deflickering advice is always appreciated, any workflows that you don’t mind sharing I would love to try.


Building a Humidifier
December 2013

Living in Colorado is awesome, I love it out here. However, the humidy is virtually non existent. We actually get very little rain or snow, because this is actually a high altitude desert.

With such low humidity, many plants are sort of difficult to grow. I needed a system to provide a high humidity zone without increasing overall room humidify beyond a certain point.

Mold is always a potential problem, so if you decide do embark down a similar en-devour do your research.

My goal is too keep the room Humidity to under 65%, with a local zone of humidity over 70%

I had looked at various humidifier systems but nothing really stood out to me. I needed something capable of delivering the vapor to a specific spot and nothing seemed to fit the bill unless I wanted to spend a LOT of money. The reservoir tanks were limited, the design not what i needed.

So i built my own. It was surprisingly easy, and not too expensive, i think i spent right around $150

The most expensive part is the ultrasonic vaporizer. I got mine off of Ebay. I got a 5 head fogger for about 90 bucks, here is a website to the manufacturer.

Ultrasonic Vaporizer

And other parts I used.

small PC fan

3 inch flexible tube

4 inch to 3 inch reducer

Humidity controller

and of course a large plastic tub with a Lid, an extension cable to cut up for the humidity controller, and a 12vdc power cable you can cut and use.


Construction was easy, got some GOOP glue, and I cut a hole out for the fan to blow air into the rub, and a hole for the 3 to 4 inch reducer. Using the GOOP I glued them together.




I cut the end off the power cable and spliced it in to the fans red/black leads, and plugged both the Fogger and Fan into a power strip that I plugged into the power cable which hit the humidifier controller.

DSCF8405 (1) DSCF8404 DSCF8406small FUJI8536

The humidity controller works like a champ. It is small, Inexpensive, and easy to use.

I plugged everything in and presto, I had a humidifier that will deliver the fog exactly where I want it.

I might have to play around with the fan though, it is a PWM fan and man, I really dont want to go through the bullshit of controlling it with PWM. right now I just use 12v, but the output is nothing impressive. So far it seems to do its job fine and it does allow me to deliver mist where I want it, but I might have to go with a bigger fan a little bit later.

So you timelapsers out there are probably scratching your head wondering exactly how i plan to work this in with timelapse. Trust me, I have this figured out and cant wait to show the process.

First, I have to build the next Greenthumb Controller.

Biolapse History Part 1

Here is the content from my last blog on this, Ill cram everything in a single page and you can read it or not, i would like to show you the past stuff in better detail, but im really looking to the future.


Unlike the rest of this blog which im sure will present backwards, this part here will just go in chronological order.


First off, thank you for checking out my project!

I have been wanting to get into Plant Timelapse Photography for quite some time now. I have been shooting time lapse photography for years now, and one of my most rewarding projects was a Hyacinth that I recorded in early 2013.

Ever since that I had wanted to do some more, but time just had not permitted. Now it is November 2013 as I write this introduction and I have been shooting plants for about a month now. Some turned out good, some turned out bad, the original plan was to put together a short time lapse film and then add a Behind the Scenes video to supplement the footage.

I still plan to do both, but I have decided to go ahead and release the project and keep a living project document that shows everything I have been doing, it will document my successes and failures as well. I had started this as sort of a blog, but I had decided that is probably not the best way to do it. It was important for me to offer a linear approach so somebody can read through this from beginning to end and see the whole story, but still allows me to update and correct mistakes, add on to various topics, and expand as I progress.

It was also important to me to provide this in a way that is easy to reference, so i have decided to sort of index everything out into various pages.

I really hope you enjoy all of this, and with any luck you will be able to learn from my own triumphs and disasters.

Original Nov 20 2013.
Last edited Nov 20 2013


Hyacinth Feb 2013

Early this year before the end of last winter I was tired of waiting for winter to end and decided to buy a grow light, a flower, and built a light controller to coordinate a time lapse of a flower. I set it all up in a room in my basement, shot for about 1 week, and ended up getting some pretty killer results.

The entire setup was pretty hokey though, luckily i have the spare room with no windows, and an old air hokey table that nobody has used in years… well.. ever really…

I purchased a 4 foot long Jumpstart grow-light off of Amazon, and spend a few hours bread-boarding out a controller. The entire thing was pretty rickety but the results were what mattered.



The controller (the jumbled mess of wires on the breadboard) was fairly straight forward. It consisted of an LCD display, 4 buttons, a relay, and two 3.5mm audio jacks which are the same style I use on the ChronoTimers.

Pretty straight forward!

Every day i would pull the memory card, dump the data, change the position of the camera and hyacinth, and start it back up.


After 4 days of shooting I decided I wanted to kill the plant, I thought showing it bloom then die would be sort of a neat timelapse. So I got some ground-kill from my shed and poured it in the plants water. it was about 50% ground-kill 50% water.

Day 5, the plant still looked good. So I added bleach to the solution.

Day 6 the plant still looked fine. I added salt.

Day 7 the plant still looked fine. So I wrapped up the shoot, turned out the lights, and started working on rendering the timelapse.

Day 8 i retrieved the plant from the room, and it still looked fine, in fact, it looked fantastic.. I took it upstairs, washed off the bulb, gave it fresh water and put it by the kitchen window to get some light. I figured after all that abuse I could just keep the flower.
Day 9 the plant limp, pale, and dead.

I really did not run into any problems, on one of the clips I was shooting at 1/320s shutter speed and got a bunch of flicker, and I did try to connect my Chronos rail up but was having difficulties getting it to trigger, i had assumed because of the breadboarded controller had a wiring problem. So i just “Ken Burns”-ed it out in post.

This was the end of my first foray into the world of Plant timelapse. It was a rewarding experience, and I really looked forward to doing it again sometime.


Getting back on the Horse
October 2013

I had been awful busy this last year, we introduced Chronos Lite earlier this year, and ran a kickstarter campaign for the Lens Apparatus. Unfortunately i couldn’t dedicate any of my cameras for a long term time lapse. After we launched the Kickstart campaign I was determined to get back into plant growth. This is also nice because I can do this from my home and I’m not really a big fan of hiking around in the cold. 😉

I figure this would be the perfect time to get back into Plant Timelapse Photography. I had recently re-carpeted my basement and that room in the basement was empty and ready for the taking. I knew I wanted to go bigger and better, the Hyacinth was a great test and learning experience, but it was a far cry from what i wanted to do. Rather than a single plant, I wanted to create entire scenes. I wanted to take this further than what anybody else has done in the past. Of course this would require baby steps. I don’t just want to jump in head first, but of course, that is exactly what I did. I had seen some beautiful plant timelapses online, there are not many of them, some of them were very well done, some looked like they were done with a low res webcam and are almost unbearable to watch due to all the flicker. I had also seen some shockingly good timelapses done by the BBC on their Life documentaries.

That is what i wanted to do, but not just that, i want to take it further, much further.

I pulled the air hockey table back out, fetched the grow lights, and this time instead of having some very fragile setup of wires on a breadboard I used a DFRobot 12×6 LCD/Button shield, a protoshield, and an Arduino micro-controller. About 6-7 hours of programming over the course of a week and i had a fairly decent little light controller. More on the controller in the next segment.

I did not simply want the black background, so i picked up some fake plants from hobby lobby and some sky blue seamless paper and worked out a little set with a mix of life and fake plants with the blue background.


The first tests were successful technically. I picked up an Orchid and some lilies, however it became readily apparent that the single 4 foot long grow light just was not enough. I replaced it with 4 foot fixture that held 4 grow light tubes. In the end, the Orchids still did not want to do squat. However that was unimportant, it was the first test run of the new controller and things worked out just fine.

So I moved the Orchids to my kitchen (where they are putting on a far better fight of survival than the Hyacinth) and went to the store and picked up some Oriental Lilies


Just a mental note, be careful if these things die. I had planned to try to change their color as I have seen others do before with food coloring in the water. Instead it just killed the flowers, but it was fun watching them wilt. The problem is after a few days they started to smell bad, and I smelled them up close and felt like I was going to vomit for the next several hours.


Greenthumb Prototype 2



I want to spend a little time going over the design and functions of the first real GreenThumb Prototype. What it is, how it works, etc.

1 Arduino Microcontroller
1 DFRobot LCD Keypad shield
1 DS1307 RTC clock module with battery
1 Relay module
1 Arduino Protoshield
1 small prototyping board
2 3.5mm jacks
1 Six pin header.
1 Optoisolator


The basic architecture is pretty easy. For simplicity sake I decided to use the DFRobot Keypad LCD shield as an interface. Im not really a big fan of the little buttons, I prefer knobs and dials, but just to make my life easier this off the shelf solution was a good fit.

The Arduino is a micro-controller. If you have never used one, it is basically a small computer that uses a variant of C programming language encased in a friendly wrapper. It has various Input/Output pins that can be used as triggers to turn things on or off, or sense weather a signal has gone high or low, or various stages in between.

The RTC Clock module is just a small clock that uses a battery to keep it on keeping track of time. It uses i2c protocol to communicate to the Arduino so the Arduino is capable of tracking time, even after being reset or a loss of power.

The Protoshield sits sandwiched between the Arduino and the DFRobot LCD keypad shield. This gives you solder connection points and access to the pins not used by the LCD shield.

The Prototyping board is soldered onto the protoshield and extends out to the side, providing a convenient spot to solder on the optoisolator, the 3.5mm jacks, and the pins for the relay.

The optoisolator is used to keep keep the 5V provided by the cameras shutter port separated from the circuitry in the GreenThumb Prototype.

The 3.5mm Jacks provide an input and output used to sync up with the ChronoTimer for motion.
The Program and Functions.

The first step was to add the proper libraries so I could use the DFRobot LCD shield, and the DS1307 RTC module. These libraries are basically a small set of routines, functions, and program that you can load onto the arduino which can save you a ton of time trying to set them all up yourself.

Next I wrote out a basic script to understand the buttons, and to build out a basic menu system, and some functions to translate milliseconds to a readable time, as well as RUN routine mode to start the program

The controller will fetch the time automatically anytime it is connected to a computer via USB.

The adjustable parameters include

1) Day time (turns on the grow lights for day cycle)
2) Night time (turns off the grow lights for night cycle)
3) Pre-shot delay (shuts off the lights before the camera is triggered during day cycle)
4) Post-shot delay (turns the lights back on after camera is triggered during day cycle)
5) Interval (amount of time between frames)

A basic routine would be as such.

Triggers camera every 10 minutes (with 10 min interval)
At 7am the grow lights turn on for the day cycle.
9 min and 58 seconds later the lights shut off (1 second preshot delay)
1 second later the camera triggers
1 second later the lights turn back on (1 second postshot delay)
9 min and 58 seconds later the lights shut off (1 second preshot delay)
1 second later the camera triggers
1 second later the lights turn back on (1 second postshot delay)
—REPEAT until 8PM–
at 8PM the grow lights shut off.
The camera is triggered every 10 minutes.

This means every time the camera takes an image, the room is pitch black. The camera uses a Hot shot PC adapter to connect to (and trigger) the Elinchrom strobe and to illuminate the subject.
There is a secondary Elinchrom strobe that triggers when it sees a flash, which is aimed up at the back wall to illuminate the backdrop.

An alternate way would be to trigger the grow-light to turn on during the Day Cycle, and off at the night cycle, but to turn ON before the camera triggers during the night cycle. I have not tried this though.

This is just the first Prototype, and I have already ordered parts for a more robust system that offers more functionality, but for what it is, it works pretty darn well.



Playing in the Dirt!
November 2013.

So the blooming Oriental Lillie was fun, but that was not my goal. The flowers were just a stepping stone into more complicated things. Small steps.


I added a few things to the setup. First off, I wanted some ground to grow on. I picked up some thick plastic to cover the table, used some old cedar posts i had to raise the trays off the table, then added four 21 by 11 inch trays. A friend of mine loaned the water pump, and i added a drip watering system that was set on a timer to feed water 3 times a day.

The first wheat grass trial was a success, now I am waiting for some things to arrive in the mail, in the meantime I am having a little bit more fun with the grass.


Running into problems

Unfortunately things do not always go according to plan, and often problems like to bring friends.

I came home yesterday and checked on the timelapse progress, only to find the water return line had skipped from its clamp and instead of dumping the excess water into the water bucket, it was dumping it on the carpet.

Luckily it appears that i only dumped a gallon or so of water onto the carpet. I shut off the watering system, used towels to absorb as much water as I could then put out a high powered fan to dry the remaining water.

I had a bowl of wheat grass seeds soaking the last few days and set the camera up to take some images of the wheat grass growing from seedling to sprout.

I checked on it few hours later to see FLASH FLASH FLASH coming from the room. Somehow the camera was just triggering every second or so as its buffer cleared. I spent some time troubleshooting, but i had to basically put everything on hold for a little while.

Plugged in Chronocontroller

-half press results in metering. camera only triggers on full press.

Plugged in Greenthumb

-Camera triggers with half press.

Plugged in Greenthumb plus hotshoe adapter with PC sync to the Strobe and plugged into the strobe it triggers non stop.

So what does all this mean? It seems I have a wiring issue on Geenthumb. If i put the chronocontroller between greenthumb and the camera i do not have this problem.

I will be building another Greenthumb controller this weekend so i can use one while i develop more capability on the other, and hopefully i will be able to clear this problem.

This is sort of how things go… sometimes everything works flawlessly, other times you rack up 3,000 shutter actuations and a gallon of water in your carpet.

Here is one of the clips that i just finished before the problems started. no audio, very raw.

Biolapse rebuild

Ill be adding content over the next few days. I scrapped the old Biolapse site.

Basically between Work, The Chronos Project, and life, I have been extraordinarily busy. I have been moving full steam at Biolapse, but the Biolapse webpage in its last incarnation was far too time consuming to manage and update. I am changing from Muse to a simple wordpress theme.  I am hoping this will make it easier to update this website, because I have some pretty cool shit going on here.  I just dont have enough time to screw around with MUSE and all the efford of getting things to line up and force a website format that does not work right for my purpose.

And with any luck ill be able to keep up with this format.