This page contains a Flash digital edition of a book.
NetNotes


Center Identifi cation Guide to Freshwater Macroinvertebrates (a nice, very basic visual guide to more common groups): http://www. stroudcenter.org/education/MacroKey_Complete.pdf . Guide to the Freshwater Aquatic Microdrile Oligochaetes of North America (more specifi c to these worms): http://www.dfo-mpo.gc.ca/Library/33909. pdf . Guide to freshwater microorganisms: https://www.msnucleus. org/watersheds/mission/plankton.pdf Freshwater Macroinvertebrates of Northeastern North America (a book I used in my undergrad to identify slimy bits in pond water) https://www.amazon.com/ Freshwater-Macroinvertebrates-Northeastern-North-America/ dp/0801496888/ref=pd_lpo_sbs_14_t_1?_encoding=UTF8&psc= 1&refRID=GE75176NY822DJV8BM3Y . As was previously stated, it may be helpful to reach out to a freshwater invertebrate lab if you are still curious. Connon T omas connon.thomas@mpfi .org Fri May 5


LM: HBO 100 light leak


I am searching on literature about the potential hazards of having light leaking out of an HBO 100 illuminator. T ere is plenty about how dangerous a mercury discharge can be if a lamp explodes. Can someone direct me or share with me information concerning the dangers of users being exposed to light leaking from a lamp housing? Mike mikegf@ hmamail.com Mon May 8


We used HBO 100 lamps in out of our Reichert MeF3 metallo- graph for several decades. Refl ected light out of the illuminator cooling vents or leaking light at the illuminator/microscope joint was never cautioned against; this was 30+ years ago, but I suppose the explanation from the factory trainer was that the internal surfaces were suffi ciently poor optical and UV refl ectors that once the light was refl ected it wasn’t a concern. Of course, the potential for permanent retina damage made direct viewing of the lamp an absolute prohibition - never ignite the bulb without the protective cover in place or look directly into the optical path. T at’s somewhat obvious to us, but the general public doesn’t comprehend the extreme brightness of these lamps. Rick Ross richard.ross@allisontransmission.com Mon May 8


TEM: LaB 6 fi laments/ cathodes


Has anyone experienced problems with LaB 6 cathodes in their TEM e.g. high dark current, beam instability? I have a vague recollection of historic issues mentioned on the List server. T e two LaB 6 that we purchased in 2014 and recently installed in our CM10 FEI TEM are extremely problematic. T e fi rst one caused an array of issues notably high dark current, beam instability fl ashing/discharging. Much trouble-shooting searching was done by lab staff and FEI service engineers—cleaning of anode, Wehnelt and insulator, and replenishing gun-insulating oil to rule out other potential causes. We also tried the spare LaB 6 cathode, which demonstrated the same issues. Installing a tungsten as a last resort resulted in the EM quickly returning back to usable status with none of these issues. I have used LaB 6 from this manufacturer for years without any problems. Perhaps it is time to move on to another. I would be interested to hear from others experiencing these or similar issues. Levina Dear levina. dear@health.nsw.gov.au Mon May 8 LaB 6 units are extremely dependent on vacuum level for their stability. Looking at the tests you have run I would be interested in the vacuum in the gun, not as given by the microscope but by monitoring as near as possible to the gun area, perhaps moving a microscope gauge nearer to that area if possible? Steve Chapman protrain@emcourses. com Tue May 9 T ank you for all the advice regarding LaB 6 fi laments. Summary of some of the responses: (i) Cleaned the legs of the fi lament (emery paper then washed with acetone) resolved the problems. (ii) LaB6 fi laments


66


have a limited shelf life. (I have not seen a use by date on any that we have purchased). (iii) Extremely dependent on vacuum level for their stability. (iv) LaB 6 fi laments, from crystals cleaving to bases coming loose - and it seems from multiple suppliers. Result: A new LaB 6 was purchased from the same manufacturer; it was installed and is working beautifully, so good to see such a bright green glow again - problem fi xed! I am waiting to hear back from the manufacturer regarding the two LaB 6 that were returned. Levina Dear levina.dear@health.nsw.gov.au


TEM:


introducing FOCUS: The interface between data collection and data


We would like to draw your attention to a new soſt ware system called FOCUS, which we fi nd quite handy to work together with automated cryo-EM data collection, as done for example with SerialEM. FOCUS is a C++ / Qt front end, running own and third-party soſt ware in the background. It features a GUI that allows you to defi ne and edit parameters and C-shell or Python scripts, which are then executed in queues. Users can add or edit their own scripts, to adapt FOCUS to specifi c workfl ows or tasks. FOCUS comes with a set of default scripts, ready to run. Installation of FOCUS requires also the installation of any third-party programs that you want FOCUS to utilize, such as IMOD, EMAN, FREALIGN, or MotionCor2, UNBLUR, Zorro, CTFFIND4, gCTF, gAutomatch, or others. If you install FOCUS on a strong Linux machine on a computer adjacent to the automated SerialEM run, then FOCUS can for example be used to: monitor the fi le system of the SerialEM run fetch newly recorded movies from the SerialEM computer, together with the pixel-defect-list and gain reference fi les, unpack the compressed movies (TIFF ZLW), gain correct, Fourier crop 8k to 4k, or to any pixel size you want (optionally) driſt -correct (with ZORRO, MotionCor2, or Unblur) computer 2D averages of the movie, and FFTs of all fi les measure defocus (gCTF or CTFFIND4) pick particles (gAutomatch) present the last recorded image and its FFT (before and aſt er driſt correction), and the driſt trajectory plot and CTF T on ring plot on a website that you would have to setup (ours is at https://status.c-cina.unibas.ch . Ours is open and shows blurred images, but you can protect it with a password and then display the crisp images) present the statistics of each recorded image on that web site (as plots over time) organize all recorded movies in a large table (similar to an Excel sheet), which can be sorted by various parameters such as grey value (which images are too dark (contaminated, beam lost) or too white (empty hole?) defocus (which images are in focus or totally out of focus?) CTF resolution (for which images is CTF determination diffi cult?) iciness (which images have a too high ratio of crystalline ice, or show devitrifi ed sample?) driſt (which images have too long or too short or too jittery driſt trajectories? which images have too high remaining interframe driſt ?) and various other parameters. T is table can be sorted by any of such parameters, and images can be moved into a TRASH folder with one click. Remaining images can be exported in folder structures and STAR fi les ready for subsequent processing in, e.g., Relion. FOCUS can also be used for tomography sessions, to: recognize parameters from the fi le name (e.g., specimen number and tilt angle) and organize fi les accordingly driſt -correct each recorded movie at a certain tilt angle, while taking the current electron dose and the prior electron dose from earlier tilt angle recordings on the same specimen into account for electron-dose-dependent B-factor resolution fi ltering compute one 2D image per tilt angle movie re-organize the tilt angle images by tilt angle (-60,-59,…,0,…,59,60) when recorded in the Hagen scheme (0,1,-1,-2,2,3,-3,-4,4,5,…60,-60) as above: monitor data collection progress on a web site, sort data, assist in manually pruning of data, export data in MRC stacks with one frame per tilt angle. Write-out


www.microscopy-today.com • 2017 September


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