A Bit of Manipulation

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mrsonchus
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A Bit of Manipulation

#1 Post by mrsonchus » Fri Oct 16, 2015 6:19 pm

Hi all, Naphthalene has inspired me to have a play-around with a couple of recent images taken from my studies of Sonchus anatomy and comparison of spp oleraceus & asper...

Here are a couple of images together with what I think are their quite-nice manipulations, basically negatives + a few parameter-tweaks, carried out with PSE V9;

This is one of the many ovules (that mature into the seeds with a 'parachute') seen within a thistle or similar (e.g. dandelion) flower head. Stained originally as seen here, with Methylene-blue stain;
An individual ovule
An individual ovule
ws_700x525_copy_sonchus.oleraceus_ovary.jpg (102.34 KiB) Viewed 7554 times
After converting to B & W and negative, with a slight green overlay and the usual boost in contrast and sharpening this rather nice detailed image popped-out of the Photoshop-machine...
ws_700x525_copy_neg_enhanced_sonchus.oleraceus_ovary.jpg
ws_700x525_copy_neg_enhanced_sonchus.oleraceus_ovary.jpg (106.9 KiB) Viewed 7554 times
This is a (Sonchus yet again - sorry) leaf XS also originally stained with Methylene-blue stain;
ws_sharpened_sonchus_leaf_1.jpg
ws_sharpened_sonchus_leaf_1.jpg (117.07 KiB) Viewed 7441 times
This is after another negative-adjust but without removing colour beforehand, subsequently I applied a couple of 'effects' to the way the negative-layer was overlaid (I think :) ) which resulted in this rather bright image which I find very pleasing and informative - I just wish I could remember exactly what I did to it after the negative-effect :oops: - I was just playing with the software really, to practice and familiarise myself with it - Naphthalene's super images were very interesting and inspired me to play-around a bit.
Center-rib of leaf in XS
Center-rib of leaf in XS
ws_700x525_copy_edited_sonchus_leaf_1.jpg (59.91 KiB) Viewed 7554 times
I quite like the effects that can be created, and so quickly too - the trick I now know to be to make a note of how you proceed!
Thanks Naphthalene for the inspiration to just have a play with some effects - PSE-V9 is clearly capable of manyu wonderful and useful things, I think I must make an effort to increase my knowledge of the use of this superb program - I've had it for about 5 years and have probably only used it for a tiny fraction of what it's capable of! Great fun. :D
Last edited by mrsonchus on Mon Oct 19, 2015 3:53 pm, edited 3 times in total.
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Re: A Bit of Manipulation

#2 Post by shawngibson » Fri Oct 16, 2015 6:26 pm

Fascinating. Love the 2nd and 4th ones. PSE is that Photoshop Elements?

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Re: A Bit of Manipulation

#3 Post by JimT » Fri Oct 16, 2015 9:29 pm

Add me to the "Fantastic" column :) I especially like the last image. Sharper and shows a lot more detail.

Now you have to go back and try to repeat the process and document it for the rest of us.

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Re: A Bit of Manipulation

#4 Post by mrsonchus » Fri Oct 16, 2015 9:49 pm

Hi Shawn, pleased you like them, it's amazing what you can do with virtually no expertise with image-manipulation software such as PSE v9 - yes that's Photoshop Elements, I couldn't (and still can't) afford the 'full-blown' Photoshop suite, but Elements 9 does an awful lot, certainly more than I actually need - also the image organizing module it possesses is really very good and importantly, I just plain like the look of it's screens, very modern and colourful, very detailed too.

I'm definitely going to learn a lot more of it's secrets, it clearly has much potential when it comes to bringing information out of microscopic images.

Here's the startup screen where you choose to edit or organize (and of course you can move between them both in use),
ws_700x525_PSE9_launch_screen.jpg
ws_700x525_PSE9_launch_screen.jpg (62.23 KiB) Viewed 7540 times
This is the Organizer screen (very powerful and fully-featured library system for images and documents),
ws_700x525_PSE9_organizer_screen.jpg
ws_700x525_PSE9_organizer_screen.jpg (66.97 KiB) Viewed 7540 times
This is the 'main-act' editor screen, a superb editing program, extremely professionally implemented and very slick indeed,
ws_700x525_PSE9_editor_screen.jpg
ws_700x525_PSE9_editor_screen.jpg (53.06 KiB) Viewed 7540 times
I don't really know about later versions, version 9 has been out for years, but I've never needed to think about an 'upgrade' to this version (9).
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Re: A Bit of Manipulation

#5 Post by einman » Fri Oct 16, 2015 9:58 pm

Very Nice. I have Photoshop CS version 9. Never learned to use it. But plan on it soon.

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Re: A Bit of Manipulation

#6 Post by mrsonchus » Fri Oct 16, 2015 10:08 pm

Hi Jim and thanks for your kind comments - I'll have another go and see if I can do it again, maybe PS has an internal record of the steps I employed to get to the image, I don't think I applied more than 2 or 3 alterations to the original....

Pleased you like them. Yes I agree re the detail, I always strive first for information from my slides and their images (although I really love a beautiful-looking stained section too! :) ) and these routines really do seem to deliver...

Must have a properly documented session over this weekend! I often make this mistake when I'm staining too - one minute I'm clattering pipettes and bottles about and the next something really special 'pops out of the process' only for me to realize that I've very little idea how it came about! :oops: I need more discipline! :)

Having a great time and am currently studying Sow-Thistles (UK) whilst perfecting (or trying to perfect at least :) ) the shortest valid (in terms of time taken that is) tissue-processing protocols for different types (in terms of physical properties such as hardness, density etc) of plant tissues, and it's going pretty well, but is a very exact and time-consuming task! :D It's going well though, my first protocol was of course from the books (Ruzin mainly) and took approx 5 days from specimen to wax-block, and the latest that I call 'extreme rapid protocol' takes (and took for the previous Sonchus ovary tissue) only 6 hours!

I love Botany and am going to change my name to 'John Shandon'!! :o :D 8-)

Back soon when I've more to share that may be interesting. :)
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Re: A Bit of Manipulation

#7 Post by mrsonchus » Fri Oct 16, 2015 10:11 pm

einman wrote:Very Nice. I have Photoshop CS version 9. Never learned to use it. But plan on it soon.
Thanks einman, yes PS is very good indeed, also I find that I simply enjoy using it! I think it's a little like an adult version of a colouring book for me! :D
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Re: A Bit of Manipulation

#8 Post by shawngibson » Fri Oct 16, 2015 10:27 pm

Cool:) I'm using Photoshop CS6 because that's what my employer bought (I make webcasts at work) but they won't upgrade now because of the new buying structure at Adobe.

I also have the NIK collection that I bought myself (plugin for PS...for lazy people like me), and I use Helicon for stacking.

I might be wrong, but I think in order to preserve History between sessions, you have to specify that in the Preferences?

Shawn

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Re: A Bit of Manipulation

#9 Post by mrsonchus » Fri Oct 16, 2015 10:36 pm

Aha - thanks Shawn, I'll have a look at this... :)
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Re: A Bit of Manipulation

#10 Post by charlie g » Sat Oct 17, 2015 1:55 am

Bravo mrsonchus/John B. , and hi all. Are you useing the microwave parathin techniques for your botanical tissues, mr sonchus?

http//microscopy.berkeley.edu/Resources/pubs/Schichnes_etal2001.pdf

Steven E. Ruzin is one of the three authors of a paper circa 2001 on: " Microwave Parafin Techniques for Botanical Tissues",

they have it 'down to six hours for processing'...err...I think.

Thank you for the wonderful microtechnique, mr sonchus! charlie guevara/ finger lakes,US

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Re: A Bit of Manipulation

#11 Post by charlie g » Sat Oct 17, 2015 1:56 am

ooops...my links rarely work...sorry, charlie guevara

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Re: A Bit of Manipulation

#12 Post by charlie g » Sat Oct 17, 2015 1:59 am

http//microscopy.berkeley.edu/Resources/pubs/Schichnes_etal2001.pdf

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Re: A Bit of Manipulation

#13 Post by mrsonchus » Sat Oct 17, 2015 4:39 am

Hi Charlie G, no, no microwave for me - that 'proper' lab equipment (e.g. the microwave for starters) is far beyond my resources I'm afraid - I've been able to drastically shorten the protocol for some, in this case the relatively soft flower-heads of Sonchus, tissue largely by virtue of the physical properties of said tissue.

Small augmentations to the process help disproportionately I find, for example the application of vacuum to fixation and dehydration stages - if these stages are carried out efficiently and properly I find that clearing is really no problem at all, I observe that any small bubbles occurring during subsequent infiltration tend very nearly always to dissipate during the infiltration. I haven't attempted to apply vacuum during the infiltration as I simply don't have the equipment needed to do this.

Such 'lightweight' tissue has performed very well for me, dissected individual florets for examination of the fascinating 'pollen-pump' mechanism typical of the Asteraceae, in this case Sonchus spp asper & oleraceus..
ws_700x525_s.oleraceus_closed_stigma.jpg
ws_700x525_s.oleraceus_closed_stigma.jpg (90.4 KiB) Viewed 7510 times
ws_edited_batch1-0013.jpg
ws_edited_batch1-0013.jpg (176.1 KiB) Viewed 7510 times
This is by far my shortest protocol, but has given consistently good results with well-chosen very fine tissue. :)
My 'extreme rapid' protocol is actually 9.5 hours :oops: (fits nicely into one day, although the resultant blocks absolutely need to 'mature' overnight in the freezer after the usual rapid-cooling of casting) as follows;
extreme rapid 9.5 hrs
FAA fixative for 3 hours

75% IPA 30mins
95% IPA 1hr
95% IPA 1hr

Histoclear 1hr
Histoclear 1hr

Wax infiltration 1hr
Wax infiltration 1hr

Cast blocks


Total time from start of fixation to block casting = 9.5hrs
Last edited by mrsonchus on Sat Oct 17, 2015 11:06 am, edited 1 time in total.
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Re: A Bit of Manipulation

#14 Post by vasselle » Sat Oct 17, 2015 8:31 am

Bonjour.
Très beau travail et très bien documenter.
Merci pour le partage.
Cordialement seb
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Re: A Bit of Manipulation

#15 Post by Raul » Sat Oct 17, 2015 7:09 pm

Wow mrsonchus you have a lot to show my friend. Please keep your microscopy passion so that we can enjoy the show :). Very nice images, I like the clarity in them, the information that you show and the simple protocols that work very well. Keep up the good work.

Kind regards, Raul.

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Re: A Bit of Manipulation

#16 Post by mrsonchus » Sat Oct 17, 2015 10:29 pm

Thanks Seb & Raul, your kind & complementary words are very encouraging to me. I've quite a lot of material to assess (sorting the ones that are worth pursuing into dewaxing etc). It's exciting to look through the many (I have about 50..) sections stretched onto slides during this stage, as every section through the dense and ever-changing tissue of the Sonchus flower-head, ovaries and indeed ovules reveals something different, especially when a single row of ovaries (of florets comprising the flower-head) as sectioned longitudinally in my posted pictures, can contain a whole series of developmental stages within those sectioned! You simply never know what you're going to reveal often. :D

Fascinating indeed to start to produce slides that actually look like and may therefore be related to, those found in the botanical books that I love and have a fine collection of.

I'm just having an absolutely superb time with my 'scope and trusty and still mighty Shandon. :D I'm very close now to being able to target my studies and produce a more cohesive piece on in this case the comparative-morphology of the Sonchus.asper and Sonchus.oleraceus 'weeds' otherwise known as the Prickly and Smooth Sow-thistles, respectively.

Shame Winter's closing in here in the UK, but I've a few specimens (among many others!) 'put by for a rainy day' in many, many jars of FAA!

Such fascinating and enjoyable times! :D

p.s. I love my jars... :geek:
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Re: A Bit of Manipulation

#17 Post by Naphthalene » Sun Oct 18, 2015 10:28 am

Nice sections, mrsonchus,
and the color inversion indeed adds some contrast!

Is your nick on the forum devoted to the Sonchus plant (I have seen it but I have met its latin name for the first time here)? Is that your favourite one?

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Re: A Bit of Manipulation

#18 Post by mrsonchus » Sun Oct 18, 2015 11:24 am

Naphthalene wrote:Nice sections, mrsonchus,
and the color inversion indeed adds some contrast!

Is your nick on the forum devoted to the Sonchus plant (I have seen it but I have met its latin name for the first time here)? Is that your favourite one?
Hi Naphthalene and thanks, do you mean my niche? My route to here, the sectioning of Sonchus, has been a very long one... I started with my lifelong love of the Taxonomy of British wildflowers and their exacting identification and comparison.

One of the very first plants I took a very close look at I now know to be a Sonchus... Simply by roving around my garden and paths etc I found a few that were obviously very similar but the questions started to form, starting of course with, 'what is this plant called?'. The close similarities and resultant difficulties with a positive ID between for example the S.asper & S.oleraceus drove me onwards as a mystery!

Now, after a lot of work and a head-long dive into histology and all it's procedures, I'm starting to be able to study plants and their comparative anatomy/morphology in an accurate and exact manner, via histological procedures.

The Sonchus were my natural first choice as they are to me most fascinating. I've gradually been building up (hopefully at least) my expertise with histology and have also used the often-featured (in my posts) Carex.pendula leaf in XS as this is a particularly easy subject for leaf XS, mainly by virtue of it's tendency to 'sit-up' nicely when being orientated in a wax-mould!

Anyway as they say, one thing leads to another and I've since looked closely at various aspects of Sonchus, roots, leaves, stems, flowers (florets) ovaries/ovules (currently being sectioned), pollen etc.

I suppose what I have discovered is that at the ''macroscopic' level of characters observable with the naked-eye or perhaps the 10x magnification offered by for example a hand-loupe, of very similar species (e.g. S.asper/oleraceus) that both exhibit a huge range of morphological variation at that level, leaf morphology, stems etc, are often not completely reliable.

A lot of these factors vary as a consequence of environmental (immediate not global that is) factors which cause changes in the way a plant's form develops and progresses as it goes through it's life cycle/s. For example, a carrot that encounters a stone will ultimately grow to be 'bent', unlike it's neighbour that was lucky enough to miss the stone and grow straight! They are however, when looked at microscopically, clearly of the same species..

But, and it's a big and exciting but, at the microscopic level we start to see characters (apomorphies often) that are constant, being the result of the genetics of the plant, and so are virtually 100% reliable when identifying two species.
This is very evident when for example, as now, looking at the structure of the cypselas of the two Sonchus mentioned above. Hence my recent sections (LS) of the flower-heads of Sonchus. I'm also learning an awful lot about the optimal conditions for a particular structure to show clear and relevant detail - such as section thickness, stain used, section-orientation etc, fascinating! :D

So I suppose at this time the Sonchus are definitely my favourites and have a huge amount of information still to be discovered, as I am nowhere near the perfection of my technique and intend to re-run the whole of my current procedures with a view to increasing the quality of my observations.
For example a good 15µ section will give a beautiful image of the overall morphology of a complete flower-head and the florets therein, but to glean fine details from perhaps individual cypselas or individual pappus-hairs a much finer (thinner) section is needed, say down to about 4-6µ, with of course the 10-12µ all-rounder sections in between.
So much to study and discover, pure fun! :D
Oh, not to mention the comparison of their pollen-grains, which I have only recently learned to section successfully! :D

The different effects, mainly fidelity, given by stains, especially in terms of their individual (and combined of course) characteristics is another whole world of discovery, for example Methylene blue seems to offer splendidly fine detail, whist TBO can in comparison appear to be a rather 'blunt-tool' in this respect... Although this may be a simple consequence of my very limited staining-capabilities at this time. :oops:

Sorry to go on so long, I'm just having a great time! :D
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Re: A Bit of Manipulation

#19 Post by Naphthalene » Sun Oct 18, 2015 11:51 am

Thank you for detailed explanation!
do you mean my niche?
I just want to correct that under the word "nick" I meant your forum nickname/account name (Mr Sonchus) - I asked since it is apparently related to Sonchus plant. I think "what is your niche" it would be rather odd question - sounds either stupid or even offensive :mrgreen: :)

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Re: A Bit of Manipulation

#20 Post by mrsonchus » Sun Oct 18, 2015 1:08 pm

Naphthalene wrote:Thank you for detailed explanation!
do you mean my niche?
I just want to correct that under the word "nick" I meant your forum nickname/account name (Mr Sonchus) - I asked since it is apparently related to Sonchus plant. I think "what is your niche" it would be rather odd question - sounds either stupid or even offensive :mrgreen: :)
Aha - I've been a bit of a nincompoop - I never thought about nickname - sorry old chap! :) Yes, it's from the plant I'm embarrassed to say... :oops:

In the only other forum that I frequent, that of 'Wild About the British Isles' or WABI as some call it, my nick is 'johnpappus' :oops: , yes I'm afraid it's a reference to the 'parachute' hairs of the Sonchus.... I know, I know, I'm a tragic case! :D

p.s. your help has served me well in the past Naphthalene, your guidance re tissue-softening has on occasion served me very well, every time I reach for the ammonia I remember your kind help. :)

p.p.s. - oh my it gets worse! I've just remembered - the 'pink thing' that is my avatar is a Sonchus.asper's pollen-grain, a rather poor image I'm afraid! :oops:
Last edited by mrsonchus on Sun Oct 18, 2015 5:36 pm, edited 1 time in total.
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Re: A Bit of Manipulation

#21 Post by gekko » Sun Oct 18, 2015 3:48 pm

Very effective manipulation and expert use of the image editor. The change in colors is validated by the fact that it improves contrast and visibility very significantly, and that the original colors produced by the stains that make visible and identify the various parts are just as arbitrary as the modified colors, so one is not modifying any "inherent" natural colors.

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Re: A Bit of Manipulation

#22 Post by mrsonchus » Sun Oct 18, 2015 5:50 pm

gekko wrote:Very effective manipulation and expert use of the image editor. The change in colors is validated by the fact that it improves contrast and visibility very significantly, and that the original colors produced by the stains that make visible and identify the various parts are just as arbitrary as the modified colors, so one is not modifying any "inherent" natural colors.
Thanks Gekko, I think it's to some degree true, the stains can be quite arbitrary in terms of indication of tissue chemistry as opposed to structure, I think it's simply a case of the common stains being perfected so long ago but so well that their use has persisted to this day, without any real hard-core research into the actual chemical (physical too maybe..) actions that the stains are involved in.

Staining really does seem to be a 'dark art' even today, but I suspect the lack of a good reason to do anything about this has meant that histology has adopted the 'if it isn't broken then don't fix it' approach to this phenomenon...

Pleased you like the images, I love experimenting to see what may be achieved this way! :D

Here are a few more, I've not had a chance to clean them up yet but they have some varied structural detail as mentioned earlier...
Overview of multiple florets
Overview of multiple florets
ws_700x525_sunday_1.jpg (116.09 KiB) Viewed 7454 times
This ovary looks interesting...
Closer into an interesting cypsela
Closer into an interesting cypsela
ws_700x525_x20_ovary.jpg (110.47 KiB) Viewed 7454 times
A closer look,
A closer look..
A closer look..
ws_700x525_x40_ovary.jpg (100.55 KiB) Viewed 7454 times
I need to study some more to identify the details, these are pictures of the Sonchus.oleraceus species... Now I need some similarly sectioned Sonchus.asper for comparison, back to my slides I think! :D
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Re: A Bit of Manipulation

#23 Post by Seb28 » Mon Oct 19, 2015 8:39 am

Very good work.
-Reichert Polyvar
-Olympus IX70
-Zeiss Photomicroscope
-Canon 600D

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Re: A Bit of Manipulation

#24 Post by mrsonchus » Mon Oct 19, 2015 3:50 pm

Now then, I've got the method for the last one, this is the little I did to the original to get this one, in PSE9:

1) start by opening your original image in PS editor
2) duplicate the 'background-layer' which will then appear on the layers-list above the original background - this is the layer to work on so select it
3) apply filter-adjustments-invert - you'll get a rather pale-looking version of the one we're after
4) then simply go to enhancements-brightness/contrast- contrast and set contrast to maximum

That's all there is to it!

I couldn't resist a play with it as I tried to recreate it so after the above I did the following...
Go to the layers frame (listing the layers) whilst having the new layer just altered selected and in the drop-down box at the top of the frame where it will say 'normal' with reference to the blending-mode of this layer, pull down the list of options and choose 'difference' - you'll be surprised to see this happen!
ws_edited_sonchus_leaf_2.jpg
ws_edited_sonchus_leaf_2.jpg (99.84 KiB) Viewed 7429 times
Great colours! What a metachromatic stain that must have been :D
Amazing what can be done really, sometimes useful and always pleasing!

Set to it - give PS a bashing, it's amazing what can be created in about 3 minutes! :D
They'd make a nice tryptych in a letterbox picture frame!
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Re: A Bit of Manipulation

#25 Post by JimT » Mon Oct 19, 2015 8:57 pm

John, thanks. I am going to give it a go right now :)

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Re: A Bit of Manipulation

#26 Post by mrsonchus » Mon Oct 19, 2015 10:34 pm

JimT wrote:John, thanks. I am going to give it a go right now :)

JimT
Go Jim!
What happened? How did it go? Show us what you've created!
I'm dying to see your creations! :D
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Re: A Bit of Manipulation

#27 Post by JimT » Mon Oct 19, 2015 10:55 pm

I am going to start a new thread with my first "manipulation". I like the result and will do more.

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Re: A Bit of Manipulation

#28 Post by mrsonchus » Mon Oct 19, 2015 11:31 pm

JimT wrote:I am going to start a new thread with my first "manipulation". I like the result and will do more.

JImT
Excellent Jim, look forward to it. :)
John B

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