All posts by thankusc

Comparing gaussian blur – 5 and 10px radius

There are some differences in the “libraries” that are used for image processing.  It is important to determine which is best for your application.  Below is a quick visual summary of 5 and 10 px gaussian blurs from a dozen or so programs.  Inkscape is missing, as I could not find the specific term “gaussian” for any blur filters.  Most of these programs are similar but some are expensive to purchase, or have a monthly contract for, others are free software.  While i really do like photoshop (two versions here) and corelDRAW and corelPhotopaint (two versions here), ImageJ is easy to use and provides pretty comparable results albeit on a very much smaller selection of effects and filters to the former programs.  The bar marker example here was a vector box (no outline) layered onto an image,  exported as a tif and processed in these programs as such.

 

 

Measuring SP-D using the “diameter” function in ImageJ

Easy to use, I found this to be the most efficient way to determine the diameter of surfactant protein D dodecamers.  I think it will ultimately be just in between the measurements that correspond to the shorter of the two hexamers, and the longer, which is where it should be.  It is a circle drawn to contact the edge (in this case, the most peripheral part of the carbohydrate domains) of three of the four.  Example below.

One dodecamer (from Arroyo et al), screen print, resampled at 300ppi, image processed in CorelDRAW 19 using the “smart blur”.  This ends up being 136.53nm, very close to what was found for 95 separate measurements of the same image (see mean and sd below)


Deviation, σ: 5.8922403533121
Count, N: 95 (separate processed images, using half a dozen different filters and effects)
Sum, Σx: 12797.82416297
Mean, μ: 134.71393855758
Variance, σ2: 34.7184963812

When the “political wish” becomes a “rosary”

Has anyone else noticed a speech pattern from the previous president.  It is like a set of words become a mantra, perhaps a meditative experience, or a soothing mantra, maybe even a prayer list, a mandala, a rosary or prayer beads. The following quote made me think of this.

This is the quote “”The county has, for whatever reason, also refused to produce the network routers. We want the routers, Sonny, Wendy, we got to get those routers, please. The routers. Come on, Kelly, we can get those routers. Those routers. You know what? We’re so beyond the routers, there’s so many fraudulent votes without the routers. But if you got those routers, what that will show, and they don’t want to give up the routers. They don’t want to give them. They are fighting like hell. Why are these commissioners fighting not to give the routers?”

Lycoris squamigera: how fast does the flower spike grow?

This lily (which i may wrongly call and august lily, but is well known as a surprise lily, naked lady, resurrection lily, but still confused with an amaryllis belladonna plant) Lycoris squamigera is one of my favorites.  Early spring dense foliage, which dies back (and helps keep weeds out of the flower bed) and then the spike and flower tip come up rapidly at the end of july (at least here in cincinnati it seems to be the end of july).  I was curious about how fast the spike grew (which seemed very fast) and searched but in the many posts did NOT FIND a single reference to any measurements.  So here is a quick and dirty estimate.

Measuring 5 stalks (not a big sample) crudely with a yardstick, at a 14 hour interval (most of it overnight) the plants can grow about one inch in 5 hours.  Also, just a casual observance, the taller the spike the faster the growth, which makes sense, because there are more cells dividing in a larger spike pushing it up faster.

I will post more measurements if i have time… LOL.

Image and signal processing micrographs of SP-D

1) The Y axes on these plots are what are generated by ImageJ…. so the y axis apparently depends upon what kind of raster file I have used to get the luminance plots that ImageJ can detect. All y axes can be (should be) normalized either to 0-100 % or to 0-255 grayscale. I don’t know if it matters, but I believe most of the existing hundreds of excel plots have 0-255 (sometimes 300) as their Y axes. THE HEIGHT depends upon all the image factors, including the brightness and ppi of the original image.

2) The X axis is variable as well, SP-D molecules just fall as they may when they are dropped onto the mica grid so there are short arms, twisted arms, touching arms, bent arms, stretched etc etc. Distance of the entire molecule i have measured as a “diameter” defined by any circle that touches three of the four edges of the cross shaped molecule. I would like the x axis to be a composite number (in nanometers) of every arm I have measured (for each microscopic technique). I haven’t gotten that final number yet, but it will be very close to 135nm with a few nm SD. So All the plots need to be adjusted to that X axis.

3) The MAIN goal here is to normalize all the plots that i have and determine mean number of peaks (with some statistical measure of likelihood) from one side of the dodecamer to the other….. and then a) find the width of each set of peaks…. b) the relative height of each set of peaks,

Amerithon challenge: Cantaloupe

Still going, after a couple minor injuries… LOL,  there was one day where i eeked out just 0.2 miles, limping and groaning.  But moving right along, getting close to half way across the USA getting near Cantaloupe Colorado, Rocky Ford region in the southeastern portion of the state.

Verge of a Dream: One candle

It kept burning.
One candle that
Held the wish.
Maybe to keep
The others from
The dark.
A shrug unapparent
To most,
for the gift
with your name
on it.
Maybe to build
Humility.
A heart may
Hold me along
With another.
One Anxious child
Amongst the smiling waves
On the gangplank
Shudders, color of
The white life saver.
Maybe it hangs like
Decoration not
To bob in the cold
Ocean.

RLB 07/17/2021

SP-D “fake” model from real micrographs and LUT tables

So the process of identifying which filters work well for image processing of AFM and TEMs (shadowed and negative stained) of molecules, it became diverted briefly into an effort to understand the algorithms of signal processing.  (the diversion was short lived, as I will never devote the time to understand them, and am not sure that an in-depth knowledge of them is required for those of us who just want to maximize the basic data that is inherent in our micrographs) I am interested in those filters that present in an unbiased and honest and searchable way (and just for fun, the image above).

The previous post (using an RGB control image to watch the erosion and dilation and alterations in pixels) examined some filters in a simplistic way. This spawned an even more interesting idea which was to use an actual “arm” (trimer) of an actual SP-D molecule as a model.  The choice of this arm is definitely biased, as it is what I have come to think is the mostly likely configuration of the SP-D trimer in terms of LUT plots.  SO while the bias in creating the initial vector illustration is mine, it is based on hundreds and hundreds of LUT plots from images processed in dozens of filters and effects in  more than 10 different image processing programs.  So it is “educated” bias.   The “raster” fill for this vector image (which is created with identical trimers — mirrored and rotated) is an actual AFM image of an SP-D trimer.  That “fake” or “control” SP-D model is below.

The N termini junction is central, beside it are four small peaks (which I am predicting) next is the alleged N-glycosylation peak (4 of them) one per trimer (about which I have not been able to find an answer as to whether this is an all (all three molecules) or none event, or 1+ 2+ or 3+ event, thus producing N glycosylation peaks of various sizes).  Lateral to that are the three predicted peaks cascading in size and width along the greater length of the collagen like domain.  Finally,  the neck (sometimes present as a slope, or small peak, leading to the CRD which definitely can be seen to have “areas of brightness and looks actually lumpy, just like the molecular models would predict”, and can be seen in the raster fill of this vector image.  Round and bell shapes are based on my observations.

The first test of a filter was made in CorelDRAWx5: Bitmap>blur>gaussian blur>10px. Image below.


And just for fun