Tuesday, 29 November 2011

07:20 – UPS showed up yesterday with a whole bunch of bottles and lids. I shoved them into the spare room that used to be full of computer gear until I have time to move them downstairs.


When we ordered the Pentax K-r DSLR, I was hoping that the Live View feature would make it easier to shoot images through the microscope, and indeed it has. Here’s Aspergillus sp. at 100X showing conidia and spores.

It’s still difficult to achieve proper focus, but much less so than it was without Live View. Without Live View, I often had to shoot literally 30 or 40 images of the same view to get one in reasonably good focus. It’s near impossible to focus on an SLR focusing screen when viewing through a microscope. With Live View, I can generally get a pretty well-focused image by shooting three or four images and tweaking the focus slightly each time.

Of course, the real problem is that for most subjects there’s really no such thing as proper focus, because those subjects are actually three-dimensional. Although many appear to be two-dimensional, most of them actually have depth. It’s often a matter of 100 micrometers or less, but that still means that when one part of the object is in focus, others aren’t, particularly at higher magnifications. Even in this image, which is a thin section at only 100X, some of those tiny little spores are sharply focused and others aren’t. That’s because some of them lie above the plane of focus, and others below.

I’ve often wondered if I should use stacking software designed for astrophotography to shoot composite photomicrographs with everything is in focus. The problem in astrophotography isn’t focus–everything is at infinity–but turbulence in the atmosphere, which changes constantly and blurs parts or all of the object. With stacking software, you shoot many images–hundreds to thousands–and then process them with the stacking software. It finds the non-blurred parts, if any, of each individual image and then combines those into one composite image. Processing an image is, of course, resource intensive, both in terms of disk and CPU. Even a fast PC may need several minutes to many hours to complete the stacking process, depending on image resolution and the number of frames in the sample.

Of course, I wouldn’t shoot dozens to hundreds of photomicrographs separately. Instead, I’d focus the microscope as well as I could and then adjust focus one direction or the other until the image was clearly out of focus I’d then turn on the Pentax K-r video mode and capture 720p video for 30 seconds or a minute as I very slowly ran the focus in the other direction. It’d be an interesting experiment, but of course the results would be low-resolution (720p), probably not good enough for publication. Also, I just don’t have time to do this. Finally, using images that were in sharp focus across the entire field would raise unrealistic expectations among readers, i.e., “What’s wrong with my microscope?”


09:42 – Amazon says they sold four times as many Kindles on Black Friday this year as they did last year. Presumably the same held true yesterday for Cyber Monday. Of course, a lot of those Kindles are Kindle Fires, which I suspect most buyers intend to use primarily as tablets rather than e-readers. Reading ebooks on a backlit display is a miserable experience, as anyone who’s used both backlit LCD and e-Ink readers can tell you. So the reality is that e-reader sales have perhaps only doubled year-on-year, if you consider e-readers to include only devices that people actually use primarily for reading.

Sales of e-readers last December were high enough to cause catastrophic sales declines for print books, particularly MMPBs, which fell about 50% year-on-year. Sales of e-readers this month should be sufficient to pretty much kill MMPB entirely, not to mention driving another nail in the coffin of trade paperbacks and hardbacks. For now, trad publishers are hanging on, although they’re doing so by raping customers with $10 and higher ebook prices and raping authors with 17.5% royalty rates. That won’t go on much longer, as more and more people, both readers and authors, come to understand that even $2.99 is a pretty high price for just a license to read a book, and as more and more titles become readily available on torrents. By this time next year, I suspect a lot of people will be trading multi-gigabyte ebook archives in the same way they started trading MP3 archives years ago.


10:49 – I just got email from a reader asking which Kindle I’d recommend, and why. There’s no single answer to that, so here goes:

If you’re a serious (heavy) reader of novels, no question, the baby Kindle 4 is the best pure ebook reader. At only $79 ($109 without ads), this should be a no-brainer for any serious reader. It’s noticeably smaller and lighter than the other models, so nearly anyone can use it one-handed, and it just gets out of your way while you’re reading. If you take notes, play games, or otherwise use a keyboard or if you want to listen to audio books, this model is a bad choice, but otherwise go for it. The ads, incidentally, are not at all intrusive. You see them only on the screensaver and as a small pane at the bottom of the screen that lists your titles. As regular readers know, I hate and despise ads, and these don’t bother me even slightly.

If you’re a serious fiction reader who does need a keyboard or listens to audio books, go with the Kindle 3. It’s larger and heavier than the baby Kindle and some people will have trouble holding it securely with one hand, but otherwise it’s a match for the baby Kindle except that it has a physical keyboard and audio support.

If you’re looking for a cheap iPad and you intend to use it only casually for reading ebooks, go for the Kindle Fire. Just be aware that, although the Fire is probably about as good for reading ebooks as an iPad, in real terms that means it isn’t very good at all.

Finally, the bastard child, Kindle Touch. This might actually have been my first choice, if only Amazon had included physical page-turn buttons. They didn’t, which means to turn pages you have to move your finger and touch the screen, which really, really gets in the way of reading. Not to mention smearing up the screen. About the best I can say for the Kindle Touch is that its virtual keyboard, which is operated by touching the keys on-screen, is a lot better than the baby Kindle’s virtual keyboard, which requires moving the cursor around using the arrow keys on the controller button. Still, if you need a keyboard, in my opinion the original Kindle 3 (now the Kindle Keyboard), with its physical keyboard, is a much better choice.

This entry was posted in biology, ebooks, photography, science kits, technology, writing. Bookmark the permalink.

19 Responses to Tuesday, 29 November 2011

  1. brad says:

    There are so many things wrong with that (Germany having to rescue Europe), it’s hard to know where to start. So I won’t – after all, we’ve discussed this before.

    A revelation to me (it shouldn’t have been, but was) was the recent revelation that various heads of State were discussing what to do about Greece more than a year ago. Yet, rather than acting, they just put off the problem until it whacked them in the face.

    Even if Germany wanted to save Europe, it cannot. The people pushing for this are, as far as I can tell, hoping to pull their personal chestnuts out of the fire – and be damned what happens to anyone else. “Oh noes, we bought tons of Greek and Italian debt, we need Eurobonds, or I might not get my bonus.”

  2. Raymond Thompson says:

    Mr. Grigg:

    The final installment of your Kindle stuff has arrived. I tried send an email to your address but the email was returned as not deliverable, the telus address that was in my email. I tried sending from work and perhaps my work address is blocked for some reason.

    Anyway, I will send your package out today. Everything will be in one box, a USPS box as USPS will be doing the initial shippping. When I have the costs for shipping I will let you know.

  3. BGrigg says:

    Ray, email showed up fine one the Telus account. Thanks for your help!

  4. Dave B. says:

    Does anyone out there have experience with trying tethering (using a smart phone as Internet access for your laptop) using Verizon Wireless? Also, has anyone used AT&T’s Uverse for Internet Access? If so, how is it for reliability and performance compared with cable.

  5. Raymond Thompson says:

    Ray, email showed up fine one the Telus account. Thanks for your help!

    I tried sending from my work address (tbp.org) and the message was bounced with this carefully crafted and very explanatory message.

    ‘bgrigg@telus.net’ on 11/29/2011 9:14 AM
    None of your e-mail accounts could send to this recipient.

    I have no real idea why my work address would not work but my personal Comcast address does work. I know a couple of times our domain has been blacklisted by an ISP. We do send a lot of email, sometimes a couple thousand in a batch. But the email is not spam and is being sent to our members who are supposed to get the emails. Sometimes and ISP will see 10 messages in rapid succession from the same domain and, wham, we get blacklisted.

    It is a pain to get off the blacklists and I have had to do so 3 or 4 times many years ago. Lately it has not been some much of a problem as I have modified our email headers and how the email addresses are formed. Seems to have helped.

    But in the case with your ISP there was something about the message they did not like.

  6. SteveF says:

    Something that may interest some: Amazon has released the Kindle source code.

  7. Larry McGinn says:

    DaveB wrote: “Does anyone out there have experience with trying tethering (using a smart phone as Internet access for your laptop) using Verizon Wireless?”

    Yep, I sure have and it worked just fine. Earlier this year, at tax time, I lost my internet connection for nearly three weeks, and my tax accountant accepts only electronic input, over the Internet. I was screwed, until I remembered I had downloaded something called VZaccess Manager. This program allowed me to go to the Internet via my BlackBerry Bold smart phone, through an encrypted USB connection. I submitted all my required data (in PDF format) and the rest is history. It wasn’t as fast as my usual cable connection, but it was fast enough.

  8. Lynn McGuire says:

    The Verizon wireless tethering works fine from my Bionic phone to my laptop, my nephew’s iPod iTouch and my Dad’s Incredible.

  9. Miles_Teg says:

    This guy, a former deputy editor of the now defunct News of the World, is completely off his head, IMHO:

    http://www.abc.net.au/news/2011-11-30/british-journo-describes-tabloid-culture-of-fear/3702966
    Unapologetic journo slams ‘scum’ NOTW editors

    Some quotes:

    “I absolutely loved giving chase to celebrities, I must admit,” he said.

    “Before [Princess] Diana died it was such good fun.”

    He said he was proud that his article on paedophiles led to civil disorder in Portsmouth and a misguided mob attacking a paediatrician.

    “In a bizarre way I felt slightly proud that I’d written something that had created a riot and got a paediatrician beaten up, or whatever was the case, due to the paedo aspect of what our readers latched on to,” he said.

    McMullan said no-one deserved privacy, calling it merely the space bad people need to do bad things in.

    “Privacy is particularly good for paedophiles, and if you keep that in mind, privacy is for paedos, fundamentally, nobody else needs it.

    “Privacy is evil, it brings out the worst qualities in people, it brings out hypocrisy, it allows them to do bad things.”

    He has also defended the hacking of the phone of the murdered teenager Milly Dowler – the case that brought the practice to Britain’s attention – saying it was not a bad thing because the investigating police were useless.

  10. Chuck Waggoner says:

    That ‘only criminals need privacy’ theme seems to get a lot of traction these days, and it appears that even Libertarians are having a hard time fighting it off. I have heard interviews with Libertarians recently, and their only comeback seemed to be that privacy should be an inalienable right. No insightful arguments as to why, though.

  11. OFD says:

    Privacy has become more and more of a joke in the last few years, especially in Perfidious Albion, yon Scepter’d Isle, etc. Where they have frigging cameras every six inches or some ridiculous figure, in public places.

    And before I wax indignant about the Brits again, my cousins, we have a small town here in northern Vermont, a village, really, near the Kanadian border, that somehow had the funds to put a bunch of cameras up in their “downtown.” Maybe it was money to burn from Homeland Insecurity handouts, I dunno. But what utter bullshit.

    And we are told that everything we type online or utter in a phone call or send in an email from wherever is all just grist for the mill, apparently. Furthermore, I have read about what it takes to get yourself out of all this now and be restored to some formerly normal semblance of privacy, and it turns out to be a veritable marathon of effort, continuously, to keep it going, once done, at nearly impossible odds, and still, still…if someone really wants to find your ass, they can and will.

  12. Chuck Waggoner says:

    Re: Uverse

    VERY reliable Internet in Indy. The radio project I am involved with, has been using it for about a year now, at the studio (sending) point. Zero down time during that period, and up/down speeds (tested regularly) have always been exactly as advertised. Significantly fewer hops to our destination than with previous commercial services that failed miserably to provide bandwidth reliability.

    I should note that we have no cable, TV, or phone aspect incorporated in that Uverse connection — it is used only for Internet. We pay a commercial rate, but I understand that the home product is exactly the same service — just minus the tech support that is available to us if something goes wrong. Nothing ever has gone wrong.

  13. BGrigg says:

    We have five new Intersection Safety Cameras here in K-town, here in the lovely and mountainous Kanuckistan frontier.

    By improving intersection safety, the number of crashes, injuries and fatalities are reduced, ensuring families get home safe and sound.

    I’m not quite sure how they work to reduce crashes. I suppose over time we will become brainwashed to slow down through the five listed intersections, thereby reducing the number of accidents ever so slightly. I’ve seen statistics that show that we are having the same number of crashes, but with far fewer fatalities and serious injuries. This is due to the car being safer, and not because the intersection is under surveillance.

    The cameras do give the cops a lovely view of the world, and the ability to take snapshots and apply facial recognition software will be quite helpful in locating common criminals, like speeders and people who turn left on the red light. Thieves and murderers who drive slowly, will go undetected, as usual.

    I plan on showing my finger to the cameras every time I drive through them, and can easily drive through all five intersections on the route home.

  14. Chuck Waggoner says:

    Speaking of privacy, if you missed the RC helicopter view of demonstrators in Warsaw on Jeff D.’s site, it is worth a look.

    http://www.youtube.com/watch?v=4HdTs-QYDGA

    Government may be putting up more cams everywhere, but here is an ordinary person getting a view no one else could see. Note the rocket being fired into the building on the left about 1:30 into the piece. Meanwhile, no one on the ground seems to notice the thing. Even among people around the landing zone, only a couple look at it.

  15. Chuck Waggoner says:

    The only coverage of the incident that I could see was in Tass. Apparently, it happened on 12 November.

    http://english.ruvr.ru/2011/11/12/60285923.html

  16. Miles_Teg says:

    Bill wrote:

    “I plan on showing my finger to the cameras every time I drive through them, and can easily drive through all five intersections on the route home.”

    Geez, who’s a Cranky Old Geezer? Your case seems to have gone from mild to severe in less than a year.

  17. BGrigg says:

    Actually, I’ve always been a rebel. I’ve been fingering the “man” since 1970.

  18. Rod Schaffter says:

    Hi Bob,

    Combine ZP is a free photo-stacking software package…

    http://www.hadleyweb.pwp.blueyonder.co.uk/

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