Diatoms from Dutch canals
Moderators: rjlittlefield, ChrisR, Chris S., Pau
-
- Posts: 13
- Joined: Fri Dec 23, 2022 9:35 am
- Location: Amsterdam
Diatoms from Dutch canals
These are some diatoms I photographed. I collected them a few days ago with a little plankton net in Amsterdam, in the canal in front of my house.
It is my first time photographing diatoms, and I had some trouble stacking them. Therefore, all these images are single shots. If anyone can shed some light on why I failed to stack these, I would love to know. Even with small stacks of 3 images, photoshop would misalign the dots on the frustules, what are some common pitfalls with diatoms? I suspect the main reason is there was too much other stuff in the water which it used to stack, I did not isolate these diatoms into clean water. Anyway, I think the single shots still turned out well, and diatoms are extraordinarily beautiful so little can go wrong.
I'm curious on people's thoughts about all the bacteria and other stuff present in the photo. Too distracting? Usually I like to see organisms in their natural environment, so I kinda like it. I did try cleaning up one of the images with a brush, though I did a whack job. What are people's thought on cleaning up images in general? Anyway, here are the photo's:
All shots are 100x oil DIC
Img0234 by Mas Jansma, on Flickr
This species has a lovely way of attaching itself.
Img0201 by Mas Jansma, on Flickr
Img0187 by Mas Jansma, on Flickr
This is such a beautiful diatom, I wonder what that line down the middle is. Is it dividing?
Img0142 by Mas Jansma, on Flickr
Img0133 by
Mas Jansma, on Flickr
Img0170 by Mas Jansma, on Flickr
Img0164 by Mas Jansma, on Flickr
Img0124 by Mas Jansma, on Flickr
You can see this nucleus dividing.
Img0088 by Mas Jansma, on Flickr
I love the two perfectly shaped compartments on this individual. They were filled with tiny dots bouncing around. Some crystalline biocompound.
Img0031 by Mas Jansma, on Flickr
The brushed up image:
diatomee_shiny by Mas Jansma, on Flickr
I think using the brush did do something good in terms of pulling attention towards the subject. Maybe if I do a better job it will look less edited.
Hope you enjoyed these images. Let me know your thoughts.
Warm regards,
Mas
It is my first time photographing diatoms, and I had some trouble stacking them. Therefore, all these images are single shots. If anyone can shed some light on why I failed to stack these, I would love to know. Even with small stacks of 3 images, photoshop would misalign the dots on the frustules, what are some common pitfalls with diatoms? I suspect the main reason is there was too much other stuff in the water which it used to stack, I did not isolate these diatoms into clean water. Anyway, I think the single shots still turned out well, and diatoms are extraordinarily beautiful so little can go wrong.
I'm curious on people's thoughts about all the bacteria and other stuff present in the photo. Too distracting? Usually I like to see organisms in their natural environment, so I kinda like it. I did try cleaning up one of the images with a brush, though I did a whack job. What are people's thought on cleaning up images in general? Anyway, here are the photo's:
All shots are 100x oil DIC
Img0234 by Mas Jansma, on Flickr
This species has a lovely way of attaching itself.
Img0201 by Mas Jansma, on Flickr
Img0187 by Mas Jansma, on Flickr
This is such a beautiful diatom, I wonder what that line down the middle is. Is it dividing?
Img0142 by Mas Jansma, on Flickr
Img0133 by
Mas Jansma, on Flickr
Img0170 by Mas Jansma, on Flickr
Img0164 by Mas Jansma, on Flickr
Img0124 by Mas Jansma, on Flickr
You can see this nucleus dividing.
Img0088 by Mas Jansma, on Flickr
I love the two perfectly shaped compartments on this individual. They were filled with tiny dots bouncing around. Some crystalline biocompound.
Img0031 by Mas Jansma, on Flickr
The brushed up image:
diatomee_shiny by Mas Jansma, on Flickr
I think using the brush did do something good in terms of pulling attention towards the subject. Maybe if I do a better job it will look less edited.
Hope you enjoyed these images. Let me know your thoughts.
Warm regards,
Mas
Re: Diatoms from Dutch canals
These are very beautiful, I enjoyed them very much.
Re: Diatoms from Dutch canals
Agree, nice selection.
Wicking the water out with tissue paper should help reduce the distance between the diatoms and the cover slip, improving resolution and limiting movement caused by the oiled objective.
In general the less detritus the better.
Nice that there is a larger image available in Flickr by clicking on image.
Wicking the water out with tissue paper should help reduce the distance between the diatoms and the cover slip, improving resolution and limiting movement caused by the oiled objective.
In general the less detritus the better.
Nice that there is a larger image available in Flickr by clicking on image.
Zeiss Standard WL & Wild M8
Olympus E-p2 (Micro Four Thirds Camera)
Olympus E-p2 (Micro Four Thirds Camera)
-
- Posts: 13
- Joined: Fri Dec 23, 2022 9:35 am
- Location: Amsterdam
Re: Diatoms from Dutch canals
Are you suggesting lowering the coverslip to the point it touches the frustules, locking the diatoms in place? That's interesting, hadn't thought of that before.
I agree the detritus is a little too much here, also since it has no colour. Next time I'll try and dilute the sample a lot. Or transfer via micro pipette.
Thanks for your kind responses!
Flickr is not ideal for me since you can't zoom in enough I feel like. Maybe I'll try the 4k link next time. But I'm worried it will take too long to load in for some people. Anyway I'll just see how it works out.
Warm regards
I agree the detritus is a little too much here, also since it has no colour. Next time I'll try and dilute the sample a lot. Or transfer via micro pipette.
Thanks for your kind responses!
Flickr is not ideal for me since you can't zoom in enough I feel like. Maybe I'll try the 4k link next time. But I'm worried it will take too long to load in for some people. Anyway I'll just see how it works out.
Warm regards
Re: Diatoms from Dutch canals
A nice set of pics with an interesting variety of diatoms.
As suggested above "clamping" by wicking out some water works well. However, even then, the raphid diatoms (with a line, or raphe, down the middle) will likely continue to move anyway. They exude a mucus from the raphe and somehow pull themselves along surfaces with that. I believe the mechanism still isn't fully understood - unless there have been new discoveries I missed.
With live diatoms, it usually isn't worth doing deep focus bracketing anyway. There is similar detail on both sides of the diatom and the deeper features will interfere with the ones closest to the objective when focus stacking. Go for a shallower stack, with fewer shots, ranging from the nearest face of the diatom "down" until the outline of the edge is sharp. Be quick about it too - even if you have "clamped" things by removing water. You'll probably get a fairly high failure rate, but stick at it and you should get your just reward in the end
As suggested above "clamping" by wicking out some water works well. However, even then, the raphid diatoms (with a line, or raphe, down the middle) will likely continue to move anyway. They exude a mucus from the raphe and somehow pull themselves along surfaces with that. I believe the mechanism still isn't fully understood - unless there have been new discoveries I missed.
With live diatoms, it usually isn't worth doing deep focus bracketing anyway. There is similar detail on both sides of the diatom and the deeper features will interfere with the ones closest to the objective when focus stacking. Go for a shallower stack, with fewer shots, ranging from the nearest face of the diatom "down" until the outline of the edge is sharp. Be quick about it too - even if you have "clamped" things by removing water. You'll probably get a fairly high failure rate, but stick at it and you should get your just reward in the end
Re: Diatoms from Dutch canals
Hi Mas, welcome to the forum!
They are very nice diatom pictures.
They must have been taken with very good equipment, would be interesting to know the microscope and its objective used and also how you couple the camera (the unsharp circular limit of the image suggests that something in the adaptation is limiting the field, maybe unwanted.
Admin note: In our forum rules there is a limit of the number of images posted, please take a look at viewtopic.php?p=518#p518
They are very nice diatom pictures.
They must have been taken with very good equipment, would be interesting to know the microscope and its objective used and also how you couple the camera (the unsharp circular limit of the image suggests that something in the adaptation is limiting the field, maybe unwanted.
Admin note: In our forum rules there is a limit of the number of images posted, please take a look at viewtopic.php?p=518#p518
The image posting limit for all Image Galleries is six (6) images during the course of one (1) calendar day. You can post one topic containing all six images, or three topics with two images each, or any other combination within the specified limits.
Pau
-
- Posts: 13
- Joined: Fri Dec 23, 2022 9:35 am
- Location: Amsterdam
Re: Diatoms from Dutch canals
Thanks you for the response, I'm beginning to see why people prefer to image dead diatoms. Though I think I will always prefer living specimens. It will be interesting to develop different techniques.
Here are some successful attempts at some diatoms that were more still than others. I'll try and embed the 24MP files, rather than HD, should take a little longer to load in, but I'm curious to see if the higher resolution is noticeable.
Diatomee_stack3 by Mas Jansma, on Flickr
I think here you can see various stages of division, some cells are bigger than others, and clumps contain different number of cells:
Diatomee_stack2 by Mas Jansma, on Flickr
Diatomee_stack1 by Mas Jansma, on Flickr
If these take too long to load I'll take them down and replace them with the HD versions
Here are some successful attempts at some diatoms that were more still than others. I'll try and embed the 24MP files, rather than HD, should take a little longer to load in, but I'm curious to see if the higher resolution is noticeable.
Diatomee_stack3 by Mas Jansma, on Flickr
I think here you can see various stages of division, some cells are bigger than others, and clumps contain different number of cells:
Diatomee_stack2 by Mas Jansma, on Flickr
Diatomee_stack1 by Mas Jansma, on Flickr
If these take too long to load I'll take them down and replace them with the HD versions
Re: Diatoms from Dutch canals
I also like to see live diatom pictures!
-
- Posts: 200
- Joined: Sat Dec 06, 2014 6:46 am
- Location: Allentown, PA, USA, Earth, etc.
- Contact:
Re: Diatoms from Dutch canals
What are the ones with the red "eye spots"? Bonus question: are those eye spots?
Re: Diatoms from Dutch canals
I would go with Euglena (That is a yes on the eye spots)Bob-O-Rama wrote: ↑Wed Mar 22, 2023 10:21 amWhat are the ones with the red "eye spots"? Bonus question: are those eye spots?
https://archive.org/details/polish-bota ... 4/mode/2up
Zeiss Standard WL & Wild M8
Olympus E-p2 (Micro Four Thirds Camera)
Olympus E-p2 (Micro Four Thirds Camera)
-
- Posts: 13
- Joined: Fri Dec 23, 2022 9:35 am
- Location: Amsterdam
Re: Diatoms from Dutch canals
Oh thanks for letting me know Pau, as you were mentioning this I was responding with 3 more pictures, this makes it look like I was just totally ignoring your comment. In the future I'll stay within the limit!
You are right I am very lucky to be in a position where I could put all this equipment together. And yes my trinocular head only supports FN22 but I notice the camera port is able to see much wider, be it with a little distortion. If people are interested I could eventually post my full setup, but before I do I feel like I should post some more micrographs. I hope these specs will suffice for now:
Olympus BX60
UPlanFl 100x oil
HR type DIC equipment
Nikon Z6 for the camera, no intermediate nothing, just plopped loosely on top of the trinocular opening. Should machine or print an adapter for more safety and parfocality.
It is still vague to me why all these adapter bits are so horribly expensive when it works so well without. I would like to get a photo eyepiece in the future to go a little deeper (I heard they can cause abberrations though). Some of the detail I see through the eyepieces is too small to see with the camera, but for now I'm super happy with where my equipment is at.
I think my technical skill in image composition, specimen preparation, stacking software, lightroom are all things I need to work on. But I think putting all the right equipment together is also part of the skill of microscopy, though I'm certainly glad that part is mostly behind me.
Bob-O-Rama yes I'm quite certain they are, they displayed very interesting motion called euglenoid motion, if you are interested look it up! In many samples I notice they crowd around the illuminated field, since they use their eyes to swim towards the light. This is interesting behaviour but can be quite distracting! Awfully impolite of the stacking software to dissect them like that, by the way. They are really very stunning organisms
In the future I will embed my photo's as 24MP, I definitely see a difference in detail.
You are right I am very lucky to be in a position where I could put all this equipment together. And yes my trinocular head only supports FN22 but I notice the camera port is able to see much wider, be it with a little distortion. If people are interested I could eventually post my full setup, but before I do I feel like I should post some more micrographs. I hope these specs will suffice for now:
Olympus BX60
UPlanFl 100x oil
HR type DIC equipment
Nikon Z6 for the camera, no intermediate nothing, just plopped loosely on top of the trinocular opening. Should machine or print an adapter for more safety and parfocality.
It is still vague to me why all these adapter bits are so horribly expensive when it works so well without. I would like to get a photo eyepiece in the future to go a little deeper (I heard they can cause abberrations though). Some of the detail I see through the eyepieces is too small to see with the camera, but for now I'm super happy with where my equipment is at.
I think my technical skill in image composition, specimen preparation, stacking software, lightroom are all things I need to work on. But I think putting all the right equipment together is also part of the skill of microscopy, though I'm certainly glad that part is mostly behind me.
Bob-O-Rama yes I'm quite certain they are, they displayed very interesting motion called euglenoid motion, if you are interested look it up! In many samples I notice they crowd around the illuminated field, since they use their eyes to swim towards the light. This is interesting behaviour but can be quite distracting! Awfully impolite of the stacking software to dissect them like that, by the way. They are really very stunning organisms
In the future I will embed my photo's as 24MP, I definitely see a difference in detail.
Re: Diatoms from Dutch canals
Lovely photos and thanks for sharing the information on your setup.
Jonathan Crowther
- iconoclastica
- Posts: 487
- Joined: Sat Jun 25, 2016 12:34 pm
- Location: Wageningen, Gelderland
Re: Diatoms from Dutch canals
Hi Mas,
Welcome, good to see Amsterdam represented on this forum!
I routinely use gelatine drops from a syringe to limit movement and to to keep my subjects as much as they will in the upper layers. Mucus should be avoided too because thicker particles tend to support the cover glass thus limiting proper flatness of the slide. Glycerine works too, but the higher refractive index has a notable effect on the transparency (increasing it). I don't know how diatoms would react to it.
Wim°
Welcome, good to see Amsterdam represented on this forum!
I routinely use gelatine drops from a syringe to limit movement and to to keep my subjects as much as they will in the upper layers. Mucus should be avoided too because thicker particles tend to support the cover glass thus limiting proper flatness of the slide. Glycerine works too, but the higher refractive index has a notable effect on the transparency (increasing it). I don't know how diatoms would react to it.
Wim°
--- felix filicis ---