Plant microscopy

Elodea movement in cells x63 obj 24/03/2018@1832

Another attempt at this – some fantastic images and video – I wonder what all those very small moving objects in the cells are? Organelles or another organism?

For photosynthesis plants use wavelengths that chlorophyll molecules can absorb, and these are blue (410-460 nm) and red (630-670 nm) light. There are 2 types of chlorophyll: a (max absorption at 430 and 662 nm) and b (max absorption at 453 and 642 nm) (



Chloroplast movement in Elodea (a form of pond weed)

Cellular Turbulence. Rhys and I went with the family to the Big Bang Show at the NEC in Birmingham. On the Zeiss stand were a number of microscopes – and on one of them some Elodea showing chloroplast movement around the cell. This pond weed has particularly mobile chloroplasts and the site is amazing. This movement is referred to as cyclosis or cytoplasmic streaming.

See the photo and video below – wow! I wonder what the small things are, much smaller than chloroplasts? Organelles or parasitic protozoa or bacteria? Magnifications here using x32 and x63 objectives so bacteria would show up at this magnification.


Some facts about chloroplasts:

Chloroplasts are organelles, specialized compartments, in plant and algal cells. The main role of chloroplasts is to conduct photosynthesis, where the photosynthetic pigment chlorophyll captures the energy from sunlight and converts it and stores it in the energy-storage molecules ATP and NADPH while freeing oxygen from water. They then use the ATP and NADPH to make organic molecules from carbon dioxide in a process known as the Calvin cycle. Chloroplasts carry out a number of other functions, including fatty acid synthesis, much amino acid synthesis, and the immune response in plants. The number of chloroplasts per cell varies from one, in unicellular algae, up to 100 in plants like Arabidopsis and wheat (from

The average chloroplast is about 3 µm (micrometers) in diameter. In one square millimeter of the surface of a leaf, there are about half a million chloroplasts (from

Chloroplasts in vascular plants range from being football to lens shaped and as shown in Figure 1, have a characteristic diameter of ≈4-6 microns (BNID 104982, 107012), with a mean volume of ≈20 μm3 (for corn seedling, BNID 106536). In algae they can also be cup-shaped, tubular or even form elaborate networks, paralleling the morphological diversity found in mitochondria. Though chloroplasts are many times larger than most bacteria, in their composition they can be much more homogenous, as required by their functional role which centers on carbon fixation. The interior of a chloroplast is made up of stacks of membranes, in some ways analogous to the membranes seen in the rod cells found in the visual systems of mammals. The many membranes that make up a chloroplast are fully packed with the apparatus of light capture, photosystems and related complexes.  The rest of the organelle is packed almost fully with one dominant protein species, namely, Rubisco, the protein serving to fix CO2 in the carbon fixation cycle. The catalysis of this carbon-fixation reaction is relatively slow thus necessitating such high protein abundances (from

Components of cells seen in photos and video:


Today’s photos and video:

If you want the wow factor go straight to the videos at bottom of page using x63 objective! I am quite excited by the views with the x63 objective below as this is first time I have used it so successfully with this microscope. The slide is turned upside down and Kohler illumination has been achieved using my “new” (second hand off ebay) NA 0.9 bright field condenser with Zeiss 475638 illuminator collimation tube (at least I think that is what it is for!).

The slide was prepared using free hand sections of Elodea leaf using razor blade put on slide with drop water and covered with cover slip. Edges of cover slip help firmly to slide by electrical insulating tape strips and then slide turned upside down and put on microscope stage (upside down as Zeiss IM microscope is an inverted microscope).

Photo of Elodea leaf section (cut free hand with razor blade) x32 objective, bright field, Zeiss IM microscope, showing cell walls and chloroplasts:

Photos of Elodea x63 objective bright field, now also shows small inclusions much smaller than chloroplasts – in later videos these are shown to move as well as chloroplasts:

Videos – first two videos are with x32 objective, bright field:

Videos – next videos used x63 objective, bright field:

Lilly pollen grains & stigma

Following are photos from a lilly flower.


x32 objective, bright field, pollen grain group, Zeiss IM microscope, Bresser 5MP microscope camera:


On another slide of similar pollen mounted with stigma I found these – I think the background yellow fluid is probably nectar from the stigma. x32 objective bright field:

The following Helicon Focus 3D model from 4 images is of the above slide shows that the pollen grain sits above the fluid on the slide, x32 objective, bright field:

lilly stigma x10 objective bright field – I have followed a strand coming out (or is it going in?) of the stigma – not sure what it is but there is a bulbous end to it:

Horizontal section Tulip stem with and without polarisation, bright field

To interpret these pictures see An excellent resource which discusses what can be found in such sections can be read at

The following image comes from this resource and is labelled to show which structure is which (Walter Dioni,

ep = skin of the stem – col = colenchyma – par = cortical parenchyma (colenchyme + parenchyma form the cortex) –cb = cambium interfasciculaire – Paq.vasc. = package or vascular bundle formed by the phloem (ph) and the xylem (xy). Later it will be seen with more details – moelle, the central cylinder of parenchyma (the pith). Cambium plus pith form a central cylinder: the stele. The raphides are oxalate of calcium needles secreted by some cells. Here, the edges of the razor blades have cut an epithelial cell full of raphides throwing them on the cuted surface

Compare these photos today with those taken through a vertical section through this same plant stem

I think the dark brown/black areas between cells in my photos below are vascular bundles seen end on, with the thick spiral supporting structure shown in the photos in my photos of the vertical section seen at the link above acting to block out light when seen end on. I can not identify raphides in the pictures below but I think I may have seen them in another post – see


My photos from today:

x10 objective, bright field:

x20 objective, bright field:

x32 objective, bright field:

x10 objective bright field crossed polarisation – varying rotation angle of one filter (below):

Comparing effect with and without Optivar

I tried adding in the Optivar into the optical train today. This is an additional magnifying lens that does the same job as a Barlow lens on a telescope. In a previous post, I noted that this particular Optivar suffers from extensive delamination so today was my first chance to find out if this is a significant issue and what difference an Optivar makes on my microscope. When I purchased it and it arrived and I found that it had the delamination I managed to get a massive discount so I am not concerned if it isn’t that good but it would be nice if it worked!

The following two pictures show an image using 32x objective bright field with and without Optivar of the cell boundary area on the tulip stem from the previous post.

The Optivar loses some of the sharpness of the image and with higher power lenses in the Optivar (it provides 1x, 1.25x, 1.6x and 2x lens – photo below with 1x lens to compare with photo without Optivar) the image is not as well focused – sadly the delamination does affect the image. Mind you, the image is not that bad and it should still be helpful for some projects.


Without Optivar:

With Optivar 1x lens (Optivar provides 1x, 1.25x, 1.6x 2x lens):

Microscopy of vertical section of tulip stem

I bought my wife some tulip cut flowers last week – an ideal place to obtain a short section of stem. The biggest problem was finding a fresh sharp blade to cut it. Ideally, a new razor blade would do the job but I did not have one to hand!

An excellent resource which discusses what can be found in such sections can be read at

Compare these pictures below to those from a horizontal section taken through the same plant stem today

In particular, see the image that author has published on that page of the spiral reinforcing structures in the vascular bundles of the stem – you can see these spiral reinforcing structures, cell walls, chloroplasts in my images below – although there are also linear artifacts from my cuts/folding tissue as I cut (basically it goes crinkly – although I floated the section on a drop of water on the slide to try and smooth this out. It is for this reason that I have not published any images of the Helicon Focus 3D depth maps – as the crinkling dominates the depth maps).


Tulip stem panorama 3176×5453 pixels below, 32x objective, bright field:

Detail of spiral supporting structure in vascular bundles x53 objective bright field:

Detail of cell wall boundary around edge of cell:

Plant stem from kitchen

The following photos show a piece of plant stem I cut up from a pot in our kitchen this evening. I don’t know what the plant was. It shows may chloroplasts and cell walls.


x20 bright field:

x20 objective Phase Contrast I annulus:

x32 objective Phase Contrast I annulus:

The following two photos are both taken using the x32 objective and phase contrast I annulus. The long thin features look like bacteria but they did not move so I wonder if they come from the plant? I wonder if they might be raphides. Raphides are oxalate of calcium needles secreted by some cells. Here, the edges of my blade may have cut an epithelial cell full of raphides throwing them on the cut surface, in a similar way to that experienced by Walter Dioni in his post on