Who Wants to Find the Right Microscope for the Right Application and Scale?
Written by Sabine K McNeill at www.3d-metrics.me
It is always fascinating to see something we
haven’t seen before. It is often mind blowing to see so much more detail that
microscopes reveal. And now it is truly ‘eye opening’ when we re-visualise
images, including those produced by microscopes, in True
Colour 3D. This is a new kind of 3D with visual
and numerical characteristics that
have metric implications.
The eye opening takes place when we tilt the Mona
Lisa painting or the colourful OKI elephant:
Mona Lisa re-visualised as
movable object in True Colour 3D – first horizontal,
'Numerically inverted' where Black becomes White and White becomes Black
Microscopy is most important for investigating
cells and MicroscopeMaster
publishes a short history of cell theory as the foundation for biological
sciences, where cells are the fundamental unit.
When our software re-visualises digital images
produced by microscopes, our fundamental unit is the number that the technology of light and colour creates. We confirm Pythagoras’: all
things are number.
As students we
may be satisfied with just seeing new aspects. As teachers we may want to
suggest systematic research into comparisons that can now be carried out thanks
to visualising Digital Colour Brightness –
the numerical representation of what the image shows: stem or blood
cells, organic or anorganic materials relating to biology, chemistry or
How to Become a Microscopist is described on www.study.com
From A to Z – Introduction to Your Microscope by MicroscopeMaster covers the field so that you can buy your own
microscope and undertake your own studies.
This article is an invitation to contribute to knowing
more by seeing more – and by using visual
and numerical comparisons to describe what
we’re seeing, observing and concluding.
Making Digital Use of the
Numerical Representation of Images
Re-Visualized with 'numerical inversion' with green as 'mountains' rather than 'valleys' as on the left
I am a
mathematician and former software diagnostician at CERN, the European Centre
for Nuclear Research in Geneva where the web was born, working with a highly
experienced developer. We are treating images as matrices of numbers.
However, every imaging
technique and every microscopy imaging technology, has its own way of
translating the physics of light and colour into the digits that represent the biology
of cells, the chemistry of elements or whatever we study under a microscope. Maybe
our own blood or skin?
representation is weighted to fit the sensitivity of the human eye. But we use
the numbers to compare images with each other numerically:
As a whole: we could immediately spot whether an image has been tampered with or
simply uses different dyes as with these stem cells below:
REGIONS OF INTEREST could be
compared: I’d like to automate our system to count blood and cancer cells and
to formulate the characteristics of cells within ‘normal’ and ‘exceptional’
then we could compare series of images
or changes over time within such series.
Horses for Courses or
Microscopy Techniques for Applications and Scale
3D is the ‘screen space’
within which to explore the look and feel of images as movable objects. This is a channel of videos recording interactions with the
- the ‘scene’
can be lit in any background colour;
- five different lights can be used to
highlight ‘virtual situations’ of
biological, chemical, physical or medical conditions;
- the ‘surface’
of the image can be coloured by giving it a different ‘tint’;
- the structure
of how the elements of the image are connected can be highlighted by making the
‘wireframe’ visible or not;
- the ‘drama
of contrast’ can be attenuated;
- and the numerical representation can be
‘inverted’ so that valleys become
mountains and mountains become valleys.
These are all user controls so that we can tell
‘image stories’ by shining the best possible lights at images as a whole and
First we had images telling us more than 1,000
words. Now we have their re-visualisations in
True Colour 3D that give us opportunities
for analysis and metrics
and thus insights and intelligence, if we have eyes to see. Many
analysts like to use data to fit their models. But when you see what is there without
bias and expectation and when you begin to interpret what you see and try to
make sense of it, then you will gain insights. Then you will understand what
the data is telling you.
You will gain the intelligence with which to interpret
what you see, for you understand how the records of a data base form a whole
picture or the columns and rows of an image become an object in True Colour 3D.
The challenge that I’d like to investigate is the quality of imaging and microscopic techniques:
- what is the range of numbers that represent light and colour as a
numerical pixel value?
- how does the magnification of a
microscope influence this range of numbers?
- are there reference images of colours
to compare imaging technologies?
Recently I wrote an article for Image Reports and discovered the International Colour Consortium in the process. Our Smart Knowledge Space offers room for ‘crowd research’ if you
Colour Brightness is
the numerical representation of images that we show in our re-visualisations. As
we progress, we will discover how to make best use of this ‘visual indicator’ to compare images and the
technologies that produced them.
To compare microscope technologies, we obviously
need to put the same ‘specimens’ under the various microscopes.
Is it appropriate to use the colour of the year images that Wikipedia publishes?
Of the techniques that MicroscopeMaster
describes, I am mentioning here only those where sample images are also
published as I re-visualised them for this article:
- Brightfield Microscopy – the
above Green Algae as sample
- Darkfield Microscope - the
above Sugar Crystals
- Phase Contrast Microscope - the
hemocytometer with fibroblasts
- Polarizing Microscope - Vimentin Protein
- Confocal Microscope - Artificial Sweetener crystals
And here ‘attenuated’
different levels of contrast.
So the principles of comparison are:
1. Visual effects
in terms of
colour and contrast;
and objects above and below a ‘zero plane’;
2. Numerical inversions resulting in
of valleys and mountains
the colour of the ‘zero plane’;
3. Numerical comparisons resulting in contrasting the numerical ranges of
magnification as it relates to
given image produced by that technique.
It is hoped that new references and standards will
be developed as a result of online collaborations between enthusiastic
microscopists who not only appreciate Microscope Master but also the marvels
that microscopes reveal.
More on Digital Imaging Here and info on Digital Pathology.
Return from Digital Coulour Brightness and True Colour 3D to MicroscopeMaster Home