Amoeba video processing

[hans]

Some more messing around with speed-up and contrast enhancement of amoeba video:


100x objective, video recorded with Nikon D5100 which has some annoying quirks related to video mode but seems to produce good quality video once set up. Have not tried to track down the cause of the banding yet but suspect interference from AC adapter. Total speed-up is 4x, 2x from combing frames 2:1 and 2x from 60 FPS playback of 30 FPS video. Using Avidemux for processing with filter configuration that looks like this:

amoeba-filters.png (100.8 KiB) Viewed 3618 times

The contrast enhancement is coming from the gamma = 0.30 setting (normally 1.00), which I think gives nicer-looking results than the actual contrast adjustment, and white balance is being done with the individual RGB gamma settings. For comparison, the original MOV video file for the first segment straight from the camera:
https://storage.googleapis.com/microbeh ... C_9308.MOV

[janvangastel]

I have also used avidemux but I didn't get good results, because for me it was too difficult to use. I did not understand the terminology. I use 'Shotcut' now. Much more intuitive and lots of 'how to' movies on Youtube. It's also freeware.

[Chris Dee]

Shotcut for me also. Nice work Hans, hopefully you can cure the banding issue.

[SWmicro]

Using Avidemux

Nice find thank you, not met that one before.
I have been playing in Virtualdub and Openshot. (Shotcut wont run for me, refuses to see two of its dlls )

[hans]

I will have to give Shotcut a try. Mainly using Avidemux because I have used it in the past for really simple stuff so already somewhat familiar with the UI. I did try Kdenlive but found the UI with large number of tiny buttons a bit cumbersome for simple usage. Main frustration with Avidemux so far was color tint mismatch between the preview and final rendering, but I think that turned out to be a graphics driver problem, not the fault of Avidemux. (At least, the problem went away when I switched output mode to not use VDPAU for hardware acceleration.)

[Bruce Taylor]

Great video, Hans! I showed it to a friend (an expert in amoeboids), who confirms that this is a heterolobosean, showing classic eruptive pseudopod formation. So, it is an amoeba, in the casual sense, but not in the group Amoebozoa.

It is looking quite likely that the flagellates in your other video are indeed the same organism, in its flagellated phase. Biflagellate heteroloboseans include Vahlkampfia, as well as the celebrity "brain-eating" amoeba, Naegleria fowleri. There's no particular reason to think this fellow would eat your brain, but all the same I would avoid putting my face in his water.

[hans]

Great video, Hans! I showed it to a friend (an expert in amoeboids), who confirms that this is a heterolobosean, showing classic eruptive pseudopod formation. So, it is an amoeba, in the casual sense, but not in the group Amoebozoa.

Thank you, Bruce. I have been trying to be careful about the amoeba/Ameobozoa distinction since my first amoeba post.

It is looking quite likely that the flagellates in your other video are indeed the same organism, in its flagellated phase.

Could this explain both flagellates -- the one showing ameoboid movement with both flagella beating and also the ones gliding with fairly rigid-looking cell shape and one flagella beating, one trailing? Or would the gliding ones be something else? I have still only seen that one showing amoeboid movement (amoebing?) with two flagellates beating. The other forms are more common but the gliding ones are difficult to get on video.

Biflagellate heteroloboseans include Vahlkampfia, as well as the celebrity "brain-eating" amoeba, Naegleria fowleri. There's no particular reason to think this fellow would eat your brain, but all the same I would avoid putting my face in his water.

Who knew amateur microscopy could be such a thrilling and dangerous hobby -- toothbrush some bricks around the house looking for diatoms, accidentally culture brain-eating amoebas on your desk...

[Bruce Taylor]

Could this explain both flagellates -- the one showing ameoboid movement with both flagella beating and also the ones gliding with fairly rigid-looking cell shape and one flagella beating, one trailing? Or would the gliding ones be something else?

My friend didn't offer an opinion about that. My own suspicion is that they are all the same heterolobosean species, possibly vahlkampfiids (the "fairly rigid-looking" one did not look particularly "rigid", to me). But amoeboflagellates are not my bailiwick. It will be interesting to learn more about them, if you gather more footage.

[hans]

My own suspicion is that they are all the same heterolobosean species...

Browsing around some more, I noticed this:
https://www.arcella.nl/naegleria-gruberi/

The size of cysts matches (10 um) and they look similar (in particular, "perinuclear layer of coarse granules") as the things (from the same sample) I was wondering about in this post:
Green algae (?) with steady internal swirling motion

Some searching relating to rotation found:
Charles F. Craig, M.D. - A NEW INTESTINAL PARASITE OF MAN: PARAMOEBA HOMINIS

The manner in which this organism becomes encysted is very interesting. The amoeboid motion gradually ceases and suddenly the organism begins to rotate very rapidly upon its axis, this rotation sometimes lasting for an hour or more. It is probable that it is during this process of rotation that the cyst wall is formed, for when rotation ceases it is observed that the organism is surrounded by the delicate, double-outlined membrane which has already been described. After rotation has ceased the organism appears slightly smaller than while in the amoeboid stage, and the nucleus is shrunken and in some instances is not distinguishable.

No idea what the modern name would be, or how closely it is related to these, but seems like rotation during encysting is at least something that has been observed before.

[Bruce Taylor]

I was wondering about in this post:
Green algae (?) with steady internal swirling motion

I agree with your "wondering", here. The final image does look somewhat like a heterolobosean cyst (to me, at least). I did a quick search of videos of Naegleria gruberia, and some of them seem to do a lot of spinning.

No idea what the modern name would be, or how closely it is related to these,

Fascinating old article! It was recognized early that this was not a Paramoeba. Gary N. Calkins moved it to the genus Craigia, a few years after the article you linked. Most of the mentions of Craigia hominis are by Craig himself (his discovery seems to have been greeted with some skepticism ). If it is a real organism, it hasn't been redescribed in a very long time, so there's no telling where it might belong...perhaps with uniflagellate archamoebae, such as Mastigamoeba, or perhaps among heteroloboseans (some do have a single flagellum though it might be a bit odd to find one in a human gut).