Monthly Archives: June 2021

Bitplanes color transform in Corel Photopaint help visualize LUT peaks along the arms of SP-D

Bitplanes-images were obtained as a filter in corel photopaint to visualize LUT peaks along the trimeric arms of SP-D (color>transform>bitplanes with slider) (original image by Arroyo et al).  It has become quite clear that there is a lot of image processing that can be done to AFM images, and with an honest approach, very little of it changes what appears in the original image.

This gif animation was made in GIMP using png files (exported from corel photopaint x5 and sized and edited in corel DRAW x5 to add the arrows that point to three distinct peaks along the collagen like domain of one of the SP-D trimers– in this case to the left of the glycosylation  and N termini peaks ).  While it is garish, the data are real. If you look at the LUT plot (made in ImageJ) from the same SP-D dodecamer in the previous post you will see the three peaks, in their typical increasing height (left to right) as those areas marked by arrows in this animation.

The tiniest (also previously undescribed) peaks that I am pretty sure exists can be seen like  “blips” on either side of the central N termini peak (on the more vertical hexamer).

Bloom and Soft glow: GIMP and surfactant protein D images

Seems like an unlikely set of parameters.  SP-D image (published by Arroyo et al) and an open source imaging program, but in fact these two filters can take a rather pixelated image from a publication and turn it into a really nice plot of brightness peaks along the arms of a molecule, examined with atomic force microscopy.  Maybe my favorite filters so far.  GIMP Filter>Blur>Gaussian 10px>Artistic>Softglow-Legacy>Glow radius 10px Brightness 0.10 Sharpness 0.75.  Green bar=100nm.  Aim: working toward a signal averaging program that will analyze these plots and determine the most likely number and size of peaks along the collagen like domain.  This plot has three on each trimeric arm of the line plotted. the CRD and neck usually comprise two peaks, a set at each end. In this particular image there is only one tiny peak beside the N termini peak… which is on the lower left arm.

Verge of a Dream: No more than one clear minute

I think all will
again be well when
the garden begun
before unforcasted
change have you
Back again to then
connect
The dreams of your
Father and talents
of the family.
I think that the
direction can be changed
releasing in
centrifugal loss
that not needed,
to become more
like Saturn, in
a ring about the planet.
I think you will,
once the swirling air
settles, know
why you were called
then, for no more
than one clear minute.
And that moment
Is maybe more but
no less than
nights, than mornings
and in between,
spent in the
eye of the hurricane,
grasping for an
answer to
hold on to.

RLB 16/19/2021

Some LUT plot tracings in Gwyddion don’t match what I find with ImageJ

Working on surfactant protein D dodecamers, the number of peaks across the entire hexamer (CRD to CRD) and specifically a tiny peak beside the N termini peak, and the number of peaks (3 or 4) along the collagen like domain (after the glycosylation peak).

I have noticed that tracings that are horizontal (at least the horizontal portion of the plot) obtained in Gwyddion looks pretty much like the plots replicated on the same image in ImageJ.  However the slightest vertical bend changes the shape of the plot completely, almost like the x axis no longer registers.  See image below.  So this dodecamer has been shown on this site many times, so i consider it a stable study.  Plots made in ImageJ are on the right, those with Gwyddion, on the left.  Each arm and a background LUT plot has been drawn and saved to excel.  (BTW, the process of saving the plots out of Gwyddion for me is a little cumbersome). Each curve was saved with a screenshot as a comparison so as to demonstrate that the actual line (segmented line in ImageJ) does not differ so much.

The same image was rotated 90o counter clockwise and then the two arms and background plots were made again.  The difference is clear.  The recommendation is to either not use Gwyddion for this type of application, or go to the forum and find out why this happens and fix it.  For me personally, I will just use ImageJ, as it is simple and straightforward.comparing LUT plots in ImageJ and Gwyddion

Cicadas: brood X, “here’s to the cute cicada clinging to a tree who in the summer’s heat chirps his melody””

June 11, I am ready for them to be “done”  ha ha. wikipedia says cicadas began about 250 million years ago. 
observations:

if they fall on their backs they must expend an enormous amount of energy to right themselves and sometimes are unable.

if they fall into a puddle it means pretty certain death because their wing muscles are not sufficient to break the surface tension of the water. I have rescued many from the cat’s water bowl and from shallow puddles in the sidewalk.

they can fly a little, haha, but not much. Most i have seen a cicada fly is about 40 feet. If one grabs them by both wings to move them to the side of the walkway and sends them air born, most just make a deep dive to the ground.  Presumably those are the cicadas that have performed their function and they have no energy reserves. (fun article on the science behind their wings)

i have seen them fly into stone walls and brick buildings. They must not have good vision, or visual processing capabilities.

Their legs are their strongest point, obviously for climbing up that tree. I did read that one website said they had 6 pairs of legs…. i tried to contact them to get them to edit it to 3 pairs (as insects have), but there was no good way to tell them.  Anyone looking at the belly up of a dead cicada shows very large legs, redish, folded neatly across their abdomens (the latter with red stripes).

I wonder if the males do the flying mostly and the females just go straight to the tree branches without venturing out.  The cicadas i toss into the air are mostly males as they chirp because of the disturbance.

i mowed grass today…. these bugs are big (thank goodness they are not the biggest cicadas (as noted below) but they are about 2.5 inches, its good they are not the loudest cicadas (as noted below) but the drone is still undeniable and kind of nice but after a long time (weeks and weeks) its a little annoying,

but they might be the dumbest… ha ha… per todays observation – any female cicada that thinks that my briggs and stratton lawn mower engine sounds like a handsome male cicada ready for mating is going to become a statistic of darwinian evolution…. survival of the fittest…. as they just fly into me, into the lawn mower and if they are down close to the wind tunnel created by the lawnmower blade they become new fertilizer for the grass… and thus dont propagate….

25 eggs (give or take) per slit, 300 eggs (give or take) per female – 12 slits per female

i have had so much fun thinking about these bugs, but ugg… ha ha… 4 more weeks and they are gone for another 17 years (well not gone, just underground preparing for their next emergence)

While these are interesting, loud, and sometimes annoying, i am grateful they are not the Emperor Cicada with a wingspan of 7 – 8 inches. YIKES. Or the Greengrocer cicada in australia which is touted as one of the loudest insects in the world.  Imagin billions of those in the air.

from the ancient literature here is an ode to the cicada: “and the tuneful Tettix sitting on his tree in the weary summer season pours forth from under his wings his shrill song”
which i have converted into a kid’s rhyme….

“here’s to the cute cicada
clinging to a tree
who in the summer’s heat
chirps his melody”