General microscopy thread.

[fragment]

I searched for Sunex DSL945D and happened across people using it to replace a GoPro lens. I'm guessing this is in combination with another lens, so maybe there's some interesting stuff that can be done with lens combos if you can work out the optics.

[JoeP]

I have a Raspberry Pi camera module. It's basically a lens and image sensor on a ribbon cable that plugs into the I/O port, and a libcamera software module that allows image and video capture. You can probably attach extra lenses like these ones to it.

[specious_reasons]

I was walking the dogs yesterday, and I noticed that the vine leaves were also getting fall "colors", so I collected a couple small ones, pressed them last night, and put them under the microscope.

Playing around, I lit the same subject with different light sources, and thought that it might look interesting if I combined the two scenes. In the image below, the left hand side is illuminated through the leaf, and the right hand side is illuminated from above.



Vine leaf, lit from above and below by Specious Reasons, on Flickr

[fragment]

Nice capture of the stellate hairs!

[specious_reasons]

I have this bush/tree thing that we cut down well over a year ago. The fucking thing won't die though, and new sprouts come up weekly. I should hire/rent a stump grinder, but I haven't.

Well, I was cutting the annoying new sprouts, and I figured it was time to put it under the microscope. It looks scary there, but it feels pretty soft. The first 2 are roughly 100X and the last is roughly 200X and cropped.

[Ari]

Wow, that’s clearly alien!

[JoeP]

[specious_reasons]

As part of my day off yesterday, I collected some lake water and put it under the microscope.

First up, the water was teeming with these:

DSC02636-2.jpg

(Paramecium species, 100X cropped)

I don't know the species of paramecium this is, but I washed my hand like 3 times after seeing this.

[specious_reasons]

Beyond those nasty protists, I found an unidentified nematode, some other ciliates, and this:

DSC02627-2.jpg
(Aeolosoma species, 100x cropped)

Something I haven't captured before! It's a species of Aeolosoma, a kind of "bristle worm". It was hard to get it in focus because it was constantly moving around.

When I was trying to identify it, I rediscovered this video:

Aeolosoma: Polka-Dotted Vacuum Worms - YouTube

[-FX-]

Thanks

[JoeP]

Any tardigrades?

[specious_reasons]

Originally Posted by JoeP

Any tardigrades?

I have bad luck with tardigrades, and they’re usually in moss and not lake water.

[JoeP]

Hence, I guess, the name moss piglets.

Your mission is clear.

[specious_reasons]

Originally Posted by JoeP

Hence, I guess, the name moss piglets.

Your mission is clear.

It's been raining for the last 48 hours, it's probably a good time to go looking.

[Ensign Steve]

[specious_reasons]

I have started a monthly practice of writing meditations on past photos. The subject of writing is inspired by a mostly annoying feature of OneDrive which is the "Your memories from this day" email. Almost every day, photos@OneDrive.com sends me a sampling of some of the photos I've taken in past years on that day. I figured that would be a nice way of picking a semi-random photo to reminisce about.

For each photo, I'm trying to remember as much as possible about the subject, setup, what my intentions were, and what went wrong, and anything else that comes to mind.

Why am I doing this? Well, because I miss it and I figured this would be a good way to rekindle interest. Also because I don't remember some of my sessions — I've been doing this for 14-15 years and I have photos but not a lot documentation, and finally just to practice writing and journaling.

Right now, it's a monthly activity, but if I get better at doing it — it's been taking me days to write and I still don't like what I have — I'll try for more frequently. Eventually, if I like what I wrote, I'll maybe make a new thread (gasp!) and post them.

Oh, and it has helped with one thing — I did spend some time with the microscope. Pictures to come...

[JoeP]

Great idea!

Originally Posted by specious_reasons

Eventually, if I like what I wrote, I'll maybe make a new thread (gasp!)

Steady on old chap.

[specious_reasons]

OK, new moss pictures:

I had a lot of dust on these, but I discovered that the healing selections I applied to one picture can be copied and pasted to another, and it worked well enough for me.

I just grabbed a small tuft of moss and whole mounted it on a slide. Here's a leaf at approximately 100X.
DSC02656.jpg

Also at approximately 100X, Two rotifers came along for the ride. Here's one.
DSC02657.jpg

Closer to the base of the tuft, in bright field and darkfield, also at approximately 100X.
DSC02661.jpg
DSC02662.jpg

And here's part of a leaf at approximately 400X.
DSC02652.jpg

For this one, I closed the condenser up as much as practical, to boost the depth of field and increase the contrast. Still, the DOF is so shallow, only a handful of cells are decently in focus. These leaves were curly and needed to be flattened to get more in focus.

[JoeP]

Originally Posted by specious_reasons

moss

You know what we're waiting for

[JoeP]

[specious_reasons]

Took a small timeout on my bike ride home today and hit a spot I frequently pick water samples from.

Man, I've let my primary microscope get dusty. I am going to have to get it serviced of learn how to do it myself. For the time being, though, I'm manually healing all the dust spots, then copy & pasting the heal data to another file. The paste, because it's applying 100s of heals, takes a long time. It takes less time than doing it manually, though.

[specious_reasons]

Here's some pictures:

First thing I tried to capture is this long, wormlike creature zooming around the slide. At first I thought it was a flatworm, because it was visible to the naked eye and shaped like a worm, but I finally identified it (probably) as Spirostomum ambiguum, a ciliate. I think this is roughly 100X

DSC03191.jpg

The next 2 are also ciliates, as yet unidentified. I think the are both the same or similar species, the main difference being what they recently ate...

I think this is 100X,
DSC03200.jpg

This was taken at 200X and then cropped.

DSC03210.jpg

[specious_reasons]

I "wasted" several hours on a simple idea. I'm looking at my current Tyvek wallet, and it's getting a bit ratty. I never liked the design on it. It's fine, but I wouldn't have picked it except it was free with a purchase. The next one is a plain color (green), and I think that might be a bit boring, so I was thinking about what to put on it, and I thought it'd be cool to do a microscope image (like I do everywhere).

Since the wallet is a color, I didn't think a color image would work, so I thought a black design might be good, and... didn't I have a GIMP script that made black & white images from a focus stack? Yes, I did! I did some tweaking and I got it to work again.

So, I posted it on GitHub:

GitHub - davebob3/gimp-photocopy-and-stack: GIMP script that creates something that looks like a drawn image from a focus stacked series.

Along with some examples. Except for the background, this is a lovely rendering of the radiolarian:

radiolarian_focus_stack.jpgradiolarian_from_script.jpg

[specious_reasons]

Actually, I think the background pattern is kind of cool.

Sorry if you remember from 12 years ago, I'm going to explain how this script works again. You start with a series of images all at different focus depths. Start GIMP and "Open as Layers" all the images. When you run the "Photocopy and stack..." script, for each layer, it will:
- Set the layer to have an alpha channel.
- Call "Photocopy" to convert the image into a black a white copy where only high contrast areas are copied.
- Convert white to transparent.

Finally, it adds a white layer in the background, so you can see how it all looks.

This is (more or less) how people hand draw microscopic subjects. They draw the in focus parts of a subject and then move the subject up or down, get other parts in focus and draw that. It's also roughly how focus stacking an image works, only good stackers align the images, handle all colors, and use fancy math to determine the in-focus parts.

There's probably more I can do with this script, like make it actually be up-to-date with the current version of GIMP, and when the images are all converted, I could align them with a GIMP function. Still, this does 90% of what I want.

[specious_reasons]

This worked better than expected:

herb_robert_stamen_focus_stack.jpgherb_robert_stamen_from_script.jpg