The Slime Mould Collective

An international network of/for intelligent organisms

How to Create Time-Lapses (and another research question)

I just had a couple of quick questions about filming slime molds:

  • How do people get videos (time-lapse) of the slime molds if they are done in well-lit areas?
    • Won't the slime mold's dry up?
    • Do they use a different type of light?
  • What type of setup is used to film slime molds (laptop, Raspberry Pi)?

I have read about many experiments using low concentrations (5 mM) of caffeine as a repelling stimulus. How do they apply the caffeine to the agar? Do they mix it directly into the agar or is it a paste that gets smeared on top once the agar has solidified?

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I use a flash - on camera flash is ok if you soften it a little with a piece of tracing paper or bounce it around with foil reflectors. For reproducibility I'd add caffeine to agar and use a punch (bottle top) to take fixed size discs. 

I was using a nikon d3100 slr with intervalometer but I think the shutter's failing after quarter of a million photos. I've now got a Canon eos-m running magic latern ( hacked firmware update) for the timing and a flash modified to run on mains. If you can find a phone with a flash that will work with a tl app then you're sorted - I've had no luck but that might be because I can't leave anything alone and put custom ROMs on all my gadgets. 

Thanks!

Is there a reason why most punches are done as cylinders and not rectangular prisms? Is it for convenience or it about how circles are easier to form tangents with?

Honestly I suspect it's just easier to sharpen a bit of pipe - you'd be amazed how much is just improvised on the moment in a lab  probably someone just grabbed a cork borer because they come in different sizes. I use a strip of staples for cutting out mazes because it works and I can't be bothered to make a proper tool 

On the drying up front - I use lens cleaner on the inside lid of my petri dishes ( anti-fog ) and prop it open ever so slightly with modeling clay to allow some air exchange. They're good for a week to ten days like that. Open agar starts to crack after a few days.

On the light side - X32 is currently under testing, I think it's 'blind' - I've had one in daylight for over a week now with no spore formation so I'm trying from sclerotia on the windowsill. If it doesn't sporulate it'll be renamed X-32 The Daywalker - could be very very useful for people doing exhibitions.

what is x32 ?

Oop, it's one of my strains. I mixed the spores of the three main strains and raised a new physarum from that - x3, this was selfed from that so became x32 - it's noticeably redder than the usual physarum. 

Hey,

I make time lapse using old mobile phone turned into IPWebcam and a Raspberry PI / server.
Here is a tutorial : https://git.interhacker.space/alban/timelapse_ipwebcam

There are many advantages to this technic :
- Old phones are cheap or even free, you can have multiple
- Old phones can to 2k picture/video or more
- Images are resized and compressed on the server on the fly, this greatly reduce disk usage
- A film can be produced while the lapse is still running

To avoid drying I tried different technic, best seems to have a clean glass over the petry, with space for air exchange like ian answer.
I also put the opened petri in a container with clay pebble and water, this lasted for maybe 24h without getting too dry.

About light, I used north windows light + flashlight, and it did not sporulate during the timelapse.
I also used a 18650 flashlight in a shoebox, it is great if you have a good quality flashlight, at low level it can last for 3 or 4 days.

On light again, DrDrey I met at the Blob expo gave me her technic : she use WS2812 LED with indirect lightning controlled by an Arduino to act as a flash. Those RGB leds are programmable so you can reproduce any light temp with it and test different white or colors.

Ill upload more time lapse in a few days.

If you're using a 'big' camera, hitfilm express is handy - it's a free video editor, ludicrously overpowered for what I need but it's easy to track and pan in shot if you're photo image size is bigger than the final video frame size. It's also got optical tracking and stabilisation so no one knows just how many times I knocked the camera whilst shooting the last one 

I shoot in a dark tent with a DSLR on an interval timer (or attached to a computer using the camera software), either under low light (LED with Neutral density filter to reduce amount of light) with slow shutter speeds or with flash heads. If you have lots of agar the moisture will slowly evaporate. keeping bowls of water nearby can maintain general humidity too to some extent.

To process the images I use a piece of software called LR Timelapse. It costs (about £250) but is worth every penny if you do a lot of time-lapses; automation with blending, deflicker and works in combination with Lightroom, so you can set key frames and programme in zooms or pans. it may be more than you need for what you want to do - there are free apps which do basic compositing.

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