AustinBlanco.com

Category: elements

  • Acquisition Speed Comparison of MetaMorph, NIS Elements, Micro-Manager

    How fast can a typical imaging system really run? What factors affect this? While most research might not require rapid sequential capture, almost all experiments can benefiet from tight exposure/illumination timing, yet few microscope users are aware of timing delays injected into experiments by the control software they are using. So how much delay is caused by software? I’ve long wanted to look into this, and finally got the chance!

    In order to accomplish this, I programmed a microcontroller to accept commands from the Lumencor Spectra-X. This high power/high speed LED engine is popular for fluorescent excitation, as a result, almost every available software application can control it. I set up my code to measure the time in which a known shutter, or known wavelength command was received on the serial line (well, USB serial).

    The team at Technical instruments were kind enough to loan me the use of their equipment, so a generous thanks to Reese Allen and the entire Technical instrument staff!

    Experimental conditions were as follows:

    • All software packages were installed on a clean OS install of Win7/x64
    • Test machine was a Dell Precision series
    • Tests were performed by configuring the camera to run ~100fps. This was accomplished using a 4×4 binning, and an exposure of 9.8mS.
    • All software applications were set to send at minimum one shutter and one wavelength change per acquisition cycle. (i.e. 1 picture from the camera, + 1 wavelength change + open shutter, then switch wavelength and cycle shutter).
    • All applications were first tested in a “free run” mode, to confirm the camera configuration was capable of 100fps at minimum.
    • No other devices were installed for these tests.

    The results were quite interesting:

    Software
    NIS Elements V4.30
    Micro-Manager V1.4.22
    Metamorph V7.8.12
    Metamorph Streaming
    Average Overhead
    60mS
    71mS
    65mS
    11mS
    Max FPS
    16
    14
    15
    90

     

     

     

    Here are some videos showing each of the programs performing. You can see some timing variation (likely caused by my capture device) but the averages are easy to resolve, and they correlate to the speed seen on the captured image stacks.

    NIS Elements

    Micro-Manager

    MetaMorph

    What becomes quickly apparent is the influence of asynchronous device control using metamorph’s “Stream” function. This is making use of a patented computer-based device sequencing technique. This technique waits for a camera “event flag” (interrupt) to fire, and when it does, a pre-defined set of events occur which control devices. This is similar to what many external trigger devices do, such as a configured national instruments card , or a pulse oscillator, or the triggerscope. The key difference here is that an external card and/or device isn’t needed, this occurs within the PC itself.

    Some further thoughts:

    • Micromanager is a great open-source competitor to other pay-for solutions. Good speed performance for a low up-front cost! (the cost of setting it up!)
    • It’s interesting that this never really seems to come up for 90% of customers who purchase “high speed” devices. Either the exposure times needed for acquisition of dim signal are so long as to never reach the speed thresholds shown here, or the capture frequency needed for a given study doesn’t require these speeds, or some other cause, but in my experience this is rarely a complaint on behalf of clients. Why isn’t this a bigger problem?
    • Many, many devices can’t reach the speeds shown here. In my tests I was using an LED driver. LED’s should have a switch time in the <5mS range. The slowest components usually found on a common automated microscope are the filter wheels and turrets, which usually run at the 50ms range when fully loaded with filters. (that’s on the fast side). So is this the reason the problem isn’t exposed more often?
    • By far, the slowest components you’ll find for microscopy are found on automated microscopes. Shutter open/close times on a common scope (i.e. big 4 name brand scope) can be in the upwards of 100ms! Moving a big filter turret usually takes 200mS. Again, this begs the question of how important speed really is for the common researcher….
    • For those who want the fastest possible speeds, have no fear! I’ll be announcing some major improvements to my triggerscope soon, to include programmable high speed sequencing capability!

    -Austin

     

     

     

  • Running HASP Licenses on Virtual machines

    One of the downsides to using OSX for my primary operating system is that most of the major imaging programs are windows-only. To compound the trouble, many of these programs, like NIS Elements, use the “HASP” license manager to communicate with a security key in order to fight piracy. So, you have to have this USB security key installed onto your system, but when attempting to use the key from a virtual machine, like Parallels or Virtualbox, you’ll see a “USB Device Unavailable” error message displayed in the VM window. To avoid this, I use the following command found at this discussion:

    1. Remove the USB Dongle
    2. Open terminal, enter the following text:  sudo launchctl unload /Library/LaunchDaemons/com.aladdin.aksusbd.plist
    3. provide your password to execute this unload command
    4. connect the dongle
    5. select your VM application, and attempt to connect to the Dongle – on my system, it worked great!
    6. Should you need to use Aladdin hasp stuff on your mac, a restart would be required, but I don’t use the alladin drivers for anything other than windows applications.

    This solution has allowed me to free my system from the constraints of requiring a bootcamp shutdown / reboot!

    -Austin

     

  • STORM comparison from UCSF NIC

    I recently received a beautiful comparison image produced by the now operational STORM system at the UCSF NIC.The sample was prepared by Michael Davidson, and was imaged by Kurt Thorn of the NIC.

    Click the image for a higher res view.

    -Austin

     

     

  • NIS Elements Fix for Sutter products Released (NIS 4.0)

    NIS 4 was released about a month ago, and the US dev team has already released a DLL fix for the Sutter Instruments product line, which I’ve uploaded here. Don’t use this unless you are running NIS E v4, AND you’re seeing a crash when adding the Lambda 10-3 to the device manager.

    -Austin

     

  • WHY YOU SHOULD ATTEND THE UCSF/QB3 Microscopy Course

    Over the course of my career, I’ve flown across the US to attend a variety of imaging related instructional courses, all on the eastern seaboard. We are all familiar with the Woods Hole courses, the AQLM course, and so forth. What has boggled my mind is that here I am in the SF Bay area, surrounded by arguably the most densely populated and diverse centers of biological science innovation on earth, and there’s no major course?

    I started pestering the owners of Technical Instruments about this one night, and they admitted the same question had long been on their minds. A few months later, we asked the NIC team at UCSF about it, and found to our surprise that they were already cooking something up. We offered to help as needed, and have been doing what we can to help support the course ever since.

    So, UCSF/QB3 has just published their official webpage for the inaugural Microscopy and Imaging Course for 2012. (They let me design the website, I hope you like it!)

    If you are a regular reader of my blog, I’ll assume you’re involved enough in imaging that you would stand to gain much from attending the course. This won’t be a “sit in classes all day” kind of deal. The course has been designed around a kinesthetic approach, with lectures taking roughly 50% of the time, and the other 50% being hands-on bench work.

    If you live far away, or are having a rough funding year, please apply for a stipend for either the course tuition and/or travel. One of the initial course goals is to host the most geographically and vocationally diverse student group possible. So if you are thinking, “my work doesn’t fit the norm for the life science community” or “I’m not from one of the major research centers”, then you should apply!

    I’ll be attending to support the course along with most of our outside team from TI. I hope to see you there!

    -Austin

  • Updating Software? A pre-chaos checklist…

    A few years after your shiny new system is installed, you’ll inevitably look at it just like you look at a car. What was once running flawlessly now has a few bugs, some dust, is slower and generally worn in. So, at some point you’ll decide it’s time for an upgrade. This may consist of new or updated hardware, probably a PC and software, but for now let’s assume all we are going to do is patch the software.

    Most software packages depend on a licensing scheme in order to run an update. If you have uManager, this won’t be a problem, but most commonly I work with MetaMorph and Elements, so I’ll be covering those exclusively.

    What version do I have?

    If you have Meta and you want to check your version and it’s capabilities, you can either call the office, or check the software update site here.

    If you have Nikon Elements, you can view your info by selecting the Elements program folder from the start menu, then clicking “Hasp Info”. Here’s what my hasp info looked like:

    If this was a consumer key, it would show an update expiration date (the date at which, once passed, new versions need to be purchased) and list the modules you own.

    Once you’ve decided on upgrade options etc, it’s time to look at what devices are installed on your system. I like to categorize devices based on how they communicate with the computer, as this is the primary factor in determining compatibility problems.

    • Serial, or USB to Serial devices and triggered devices  – Serial devices will be connected via a 9-Pin cable, and will use a COM port on the computer. You can check COM ports using windows device manager. USB falls into two general categories – Serial Emulators or direct drivers. USB to Serial Emulated devices simply create a fake serial port at the device side, so when you plug the device in and power it, you’ll see a new COM port appear in your ports list under windows device manager. Some systems, like the Sutter 10-3, use a driver which allows you to select either VCP (Virtual Com Port) or driver-only. Triggered devices use TTL signaling to communicate, and typically are connected via BNC cables to either another device or a custom board on the PC, so this could mean life is easy or hard, depending on what you have.
    • USB Driver Devices – Any device which, once loaded, appears in the windows device manager under it’s own category, uses a direct driver. A good example would be a Ti-E microscope. You’ll find the scope appear under “Imaging Devices”. While generally speaking, USB connected devices are straightforward to work with, it would be prudent to confirm that the firmware of the device, and the driver version for the device, are both compatible with the new version of software you’ll be installing.
    • PCI/PCIe Card Devices – Cameras usually fall into this category more than anything else, but there are devices such as an Andor Revolution Laser Combiner, or a Mosaic Illumination system, that also require the use of a card installed in the computer. For these devices it’s important to check firmware and driver support for your software upgrade, and it’s extremely important to consider the card type, it’s height requirements, and it’s connector (like PCI vs. PCie x16 etc) when purchasing a new computer.
    Note the "Virtual Com Port" vs. the standard "communications port". The former is a USB to Serial Adapter.

    Once you’ve collected the above info for each device which is run through your imaging software, you can go through a straightforward checklist of the required communication items for that device. Keep in mind that for most software companies, they build a driver for a given instrument at a single point in time, and don’t update that driver until there is a good reason to do so. Version changes between the software, firmware, and drivers may cause problems, so we’ll investigate this entire chain for our devices:

    1. What is the version number of the software you’ll be upgrading to?
    2. For that version of software, what are the driver versions required for your devices? In Meta, you can view the Supported Hardware page, to check the minimum version for your device. Nikon has a support document, which can be found on the download site (enter any username, and your Hasp ID for the password), under “Device/Camera/Firmware Documents, or just click this link after logging in.
    3. If your device driver needs to be upgraded, does the firmware in your device need an upgrade as well? This can be investigated by contacting the device manufacturer.
    4. Is either the device manufacturer, or the software developer, aware of known major bugs or issues with the versions you’ll be upgrading to? Normally there are always a few bugs, the question is whether or not they’ll be a problem for your work.
    5. If you are considering moving from an x32 to an x64 system, make sure to check for 100% support in x64, I’ll be writing more on this on a separate post, as it’s a constant problem for me right now.

     

    Example of a Supported device on Meta's hardware page. Note this device says it is not supported in Windows x64!

    Armed with the answers to the above questions, you’ll be well prepared to perform an upgrade on your instrument! As always, you may wish to do this yourself, or pay your local sales rep to take on this headache. As a general rule software upgrades are a lot of work, and provide a chance to break an otherwise functional system, so service and sales reps are understandably wary of upgrades. You can help your rep a lot by bring this info to them at the beginning of the upgrade process (or at least providing the version #’s and device types on your system).

    This process will obviously take some time to complete, but it’s a very small investment to reduce the chance of the system going down due to a half-update, or performing the update only to find some major bug which will render the system unusable! You’ll never guess how I learned to be wary of this…:-) Ultimately, software updates can provide new capability, fix bugs on the device or software side, and are an important aspect to the overall maintenance of an instrument. With proper planning, the operation can go from chaos to an enjoyable experience.

    – Austin

     

     

     

     

     

  • Lumencor Sola Driver for NIS Elements

    Yesterday we received our first shipment of Sola white light LED driven sources for microscopy. I had a chance to snag one and write a driver for it. Price is $300 USD. The driver controls both the shuttering and  ND on the box, and integrates easily into Elements as a shutter and ND filter wheel.

    Please contact me if you are interested!

    -Austin

     

  • PhotoFluor 2 Driver for Nikon Elements

    89 North has asked me to cook up a driver for the PhotoFluor 2, which I am now hosting under my Macros & Journals page, or you can use this link. This driver works in NIS Elements AR, and BR with Advanced Interpreter.

    Please contact me if you have any trouble using it!

    -Austin

     

  • Lumencor Spectra Driver Available

    Spectra

    I’ve written a Lumencor Spectra Driver that works with NIS Elements B3.2+. (AR or BR + Advanced Interpreter) The driver provides integrated control into elements for both intensity of lines and channel. These appear as a shutter and two filter wheels, offering full integration into Elements’ Optical configurations. We are selling it for $750, including online install on your system. Please contact me if you’d like to try it out!

    Screenshot of Filter & Shutter Interface

    -Austin

     

  • Acquisition crashes, and power settings in Win7

    Windows 7 has a new power management interface, and the design of modern motherboards, along with win7 Automatic Power Management (APM), can cause some insidious device-based software crashes if power options aren’t set correctly. Here’s how to make sure your system is running in the best mode.

    • Open the Windows Control panel
    • Search for and open “Power Options”

    • You’ll see a “power plan” like the one below. Click the “Show Additional Plans” button, and check the radio button for the “High Performance” plan.
    • Click on the “Change Plan Settings” link, then click “change advanced power settings”.  This window is where the real control over the power plan exists.

    • Browse through each item provided, and set power management to either disabled, maximum performance, or off, depending on the item. Things like turning off the hard drives are a bad idea on an acquisition system, as this can cause problems with long term timelapse.
    • One key item is the PCI link state power management. This should be set to “Off”. This item selectively disables power to the PCI bus. Some of the cameras and devices used in acquisition systems rely on PCI / PciE based cards to operate, and cutting power to these cards can cause all sorts of havoc.

    • Another common problem, probably the biggest I’ve seen, is the USB suspend entry. Again this function turns off the USB bus when not in use. This has caused crashes in software when operating USB devices, so it should be set to “Disabled”.

    • Once you’ve investigated each item and made any desired changes, click OK, and then close out of the power option windows.

    Making the changes noted above should make a big impact on the stability of your imaging system. Hopefully this guide helps you to avoid acquisition crashes on your system!

    -Austin

  • Back up your NIS Elements settings! (V3.1+)

    (Updated 5/6) – One of my colleagues (Thanks Aaron) noted that the exporter/importer only works on v3.1 and higher.

    So in the past week I’ve had two systems that mysteriously lost all device settings from elements. I am suspecting this is due to a waindos security update somehow, but until this is confirmed the simple, easy and safest method to ensuring you’ll be able to get back up and running quick is to use the Elements Settings export/import tool.

    There are 32 and 64 bit versions of this tool, and it’s extremely easy to use.

    1. Download the tool from my files & info page.

    2. Install the software.

    3. You will now find a new item in your start menu -> program files -> NIS-Elements folder, called the “NIS Settings Tool”. Open this program.

    4. You will see export and import tabs for this tool, so export all settings to a file, and keep it handy in case you need it!

    What’s nice here is you can basically lose the entire NIS-Elements install for any reason, and be back up just by loading the settings back with this tool.

    – Austin

     

  • Voltage output from NIS Elements, MetaMorph or uManager for under $200

    USB-6008 connected to my multimeter

    I posted briefly about this a while back, in my explanation of the demise of the parallel port. I finally got my hands on a National Instruments USB-6008 box, and have found the unit to be 100% compatible with any NI-DAQ controlling application. What follows is an example of how to set this up using NIS Elements.

    First – what types of devices could be controlled with this?

    • AOTF Controllers (Spectral, Neos, Etc.)
    • Single Shutters (Uniblitz Etc)
    • Piezo Z Controllers (ASI, MCL)
    • Directly driven 0-5v lasers
    • Monochromaters
    • LED Light Engines (Lumencor/89 North)

    So – this thing is great when compared to the PCI cards normally used for numerous reasons:

    • Cost – This is ~$160 USD, vs. the PCI/PCIe cards running $1,500+
    • Size – This box is quite small, doesn’t require a huge cable or breakout box, and doesn’t occupy a slot on the PC
    • Portable – this will work on a mini form factor PC, or a laptop (which is what I used for this post), instead of requiring a full size tower

    Installation:

    Install is a snap. The only hard thing to do is place the pin indication stickers in the correct orientation on the box. If you mess this up you can always refer to the manual, but the little sticker strips included with the box make field-modification much easier. After this run the NI installer and reboot. Finally, connect the USB cable. The box will appear, and if you like, you can launch one of the NI test apps to run the device.

    In Elements, we’ll re-run the installer and check the “National instruments” hardware group, then select “NI DAQ”.

    Next, open Elements, open the devices window, and add the NI Device.

    Once we add the device, and click configure, we can define what each of the inputs and outputs do. Here I’ve selected a 2 line AOTF.

    After you’ve dialed in the settings you want, close the window(s) and if you don’t see the new device control panel, right click and select “acquisition controls” to find it. In my case the AOTF Settings window popped up after closing the device window.

    I also  made a short guide to using this box in elements via the Youtube video below. ***In the video I mention this thing costs $130, which is incorrect. It’s listed on the NI site as $168 as of today. Also I have yet to test more than 1 unit, but will be doing so shortly…

    httpv://www.youtube.com/watch?v=poKZjRgWdhQ

    One point of discussion is devices that require a 0-10v range. I’m looking into using a small powered op-amp chip and maybe packaging it into a small box for sale, or at least I’ll write up a how-to on using one, for people that need this voltage range. Luckily most of the devices out there can accept 5v or 10v input. Overall I’m happy to see NI is moving beyond PCI and PCIe bus cards. USB based boxes like these lower the acquisition cost for the customer, provide everything we need in the life science world concerning speed, and open up access to a wide array of devices. I’m looking forward to using this box on future systems!

  • Nikon C2 – NIS Elements and Spectral Capability

     

    Nikon has redesigned and updates it’s classic C1 Confocal. The C1 was a great core facility confocal as it was a stable and reliable product. The one thing that held it back was the lack of access to NIS Elements software. With the release of the C2 this problem has been solved. So, along with a comprehensive timelapse multi site capability, users can also stitch using a high power objective, on multiple sites and with multiple channels.

    Example showing large image capability

    The C2 also brings spectral options and DIC options to the package, and it looks like Nikon is offering it at a very competitive price. It will be interesting to see how the access to Elements will affect the market performance of this instrument. I’m thinking it’ll do well.

    – Austin

  • Proper RGB Conversion of Multichannel Images

    When acquiring images in NIS Elements, it is possible to acquire each image with a color over that is approximate to the wavelength used for acquisition. This is the easiest way to view and relate multi-channel data, but when converting the images for export to other programs, it cam become a problem.

    In the image below I have two channels acquired – DAPI and FITC. If you note the overlay each of the two channels are completely independent.

    Original 2 Channel Image

    If I now use the Image -> Convert -> Convert to RGB command, some of the green and blue signal will be mixed within each other, and some of each channel will mix into the red channel:

    Image Converted to RGB and now color mixed

    So what causes this? If you note the channel data in the original image, the color is not a pure green. The 488nm and 405nm alexa dyes actually emit in blue-green hues and green-orange hues. So if we were to attempt to measure signal intensities in the RGB image using another program, our measurements would be invalid. In order to avoid this, you can  modify and use this macro, which will force the channels to pure Blue, Green and Red colors. With these color settings no color mixing will occur in the conversion.

    – Austin

  • Nikon DS U3 Series Controller Install Guide

    DS-U3 Controller

    The new Nikon controllers for DS Series Cameras run on Firewire. As with other firewire adapted imaging cameras, there are numerous

    small issues to awtch out for during the setup and operation process. Once they are up and running, they should be fine – but for those of you who perform installations, you’ll probably find this info handy:

    Here’s the Install Guide for the DS-U3 controller. Follow each of hte steps included to insure a correct installation of the unit.

    – Austin

     

  • Determining background sources in fluorescence

    For microscopy engineers and suppliers like me, the background produced in an image is of importance, if that background is created by the imaging system itself. What so many of us on this side of the scope (vs the user side) forget to train on and talk about is the specimen side of the background. So, how can you figure out where the background is coming from in your image?

    Example of two noise sources, one distributed and the other localized.

    Background Sources

    Usually background sources mentioned are those produced by the imaging system. I’d like to cover instead those produced by the specimen and the imaging system. These can be:

    System Background Sources

    • Fluorescent filter crosstalk/performance limitations
    • Objective and other optical limitations (aberration/convolution etc.)
    • Camera measurement noise (A/D Read Noise)
    • Camera-produced background noise (heat that the camera sees as signal)

    Specimen Background Sources

    • Auto-fluorescence produced by cells and/or media
    • Refraction/reflection of excitation light by specimen container (think plastic multi-well plate)
    • Ambient light in the room where the microscope is located
    • Byproduct remaining from sample preparation protocol (stain that remains after a rinse, etc.)

    Identification and Removal

    Instead of reviewing each noise source type and it’s cause, let’s instead perform a gross identification scheme to determine where the greatest noise source exists.

    Method 1: System vs. Specimen Measurement
    1. Configure your microscope and imaging system, and place your specimen on the scope.
    2. Focus on your specimen.
    3. Acquire 2-3 images of various locations of the specimen.
    4. Remove the specimen from the microscope entirely, not changing the scope at all (don’t drop the focus or change filters).
    5. Acquire 2-3 images with the scope in this state.
    6. Using either the ROI tools, or other tools available in your software of choice, measure the average intensity value, for the non-exciting area of your 2-3 specimen-present images, that we acquired in step 3.
    7. Measure the entire image field of the  2-3 images we acquired in step 5.
    8. We now have an intensity measurement of the amount of background for the imaging system + specimen, and the imaging system only.
    • If the image intensities remain relatively unchanged between the two image groups, the source of noise is in the imaging system.
    • If the intensities from the images in step 5 are significantly lower than those from step 3, noise is being produced by the specimen, or specimen container.

     

    In my next post I’ll cover how to further pinpoint noise sources, and how to eliminate them.

    – Austin

     

     

  • *UPDATED* Micro-Manager Tethered to a Nikon Digital SLR

    ***UPDATE 3/3/2014***

    After a few requests for a report on x64 capability using this tethering technique, I tried installing the NK Remote software on a rather fresh copy of Windows 7×64 – it did not communicate with the camera at all. On the other hand, the open source application “DigiCamControl“, worked perfectly. Now, as far as micro-manager goes, there isn’t a connection from DigiCamControl to micro-manager. So – short term solution is to run the proposed setup below on an x32 system – if anyone gets x64 working please post here!!! -Austin

    So I had a customer interested in a macro application for scanning. In some cases, applications like these don’t require a telecentric optical system such as the AZ-100, nor do they fit into a typical stereo microscope application. So, what to do? Well, when your object for imaging is too large for a microscope, one option may be a macro lens on a digital camera. Something like this:

    Copy stand for SLR

    This type of system will allow for a stable focusing and zoom setup, but is limited in magnification power and light control. In some cases though, this is the way to go.

    The next problem is that of focal and positional control. No microscopy device control software available, such as elements or metamorph, supports non-scientific grade cameras. So, how do we position a specimen under this camera in an automated fashion? Well, it turns out micro-manager has a plugin available for such work, and it’s available in the nightly builds here .

    What you end up with is a camera that can be controlled from a laptop, along with a stage, z motor and other automated imaging hardware. Here’s an example of my setup running on a windows 7 x64 laptop and a D80.

    D80 and Win7 x64

    Requirements

    This setup requires the following items:

    1. Suitable camera and lens (see below)

    2. Copystand for camera.

    3. Computer for control.

    4. External power supply for camera or a battery extension (more for ease of use but I consider it a requirement).

    5. USB Cable to camera.

    6. Control Software for interfacing to uManager. This is pay-for software, found here. The software currently ranges from $90-180.

    7. A right angle view finder isn’t required, if you don’t mind a stiff neck!

    Setup:

    So, follow the instructions found here for setup. My summary of setup, which took a whopping 5 minutes (this is amazingly quick for open source software!) went as follows:

    1. Download Breeze Systems trial for NKRemote & Install.

    2. Download nightly uManager build & Install.

    3. Set camera to PTP mode.

    4. Run NKRemote and snap image to confirm communication with camera.

    5. Run uManager. Edit hardware seup using the “Setup hardware” tool and removed the demo camera, and added the NikonDSLR.

    6. started snapping images! Here is an example of running in uManager (click on the picture for a higher res version):

    Nikon D-80 acquiring images in uManager

    What cameras are supported:

    All of the basic DSLR models from Nikon are included with the NKRemote software. Tethercam is the driver used for the uManager side, and it states an “incomplete list” of cameras as follows:

    Nikon D7000, Nikon D90, Nikon D5000, Nikon D300, Nikon D300s, Nikon D700, Nikon D3X, Nikon D3s, Nikon D3, Nikon D200, Nikon D80.

    Lenses to Use:

    Some lenses that work as portrait lenses like a Nikon 50mm will work adequately as macro lenses. On the other hand, it’s recommended to shell out the extra cash for a well-made macro lens, such as this one. The nice thing about working with commonly available photo gear is that in many cases you can even rent lenses to see what works best for the job at hand.

    This was a fun and quick test and I am excited to see how this capability is used for macro work in the future!

    -Austin

  • Fix for Elements v 3.2 and ASI Stages

    As anyone who is running NIS Elements v 3.20 + is aware, the ASI stage controllers of any MS-2000 series will not be usable once elements issues a connection command to the controller. Elements will control the stage properly, however the user will not be able to position the stage using the manual joystick. So, the guys at ASI have found the cause of the problem and have issued a series of firmware updates that will fix a variety of controllers.

    ***DISCLAIMER*** –

    These files MUST be used on the correct controller. If you use the wrong file it could cause some serious problems for your controller/stage/software. So, call ASI or shoot me an email if you have any doubt whatsoever about this. Basically, if you had any custom option on your stage (inverted axis, non-standard lead-screw or other modification) CALL ASI and give them your serial # so they can make sure everything will work for you.

    Or, better yet: make your direct or dealer rep do the patch. That way they can take the blame if they screw things up 🙂

    Required Items:

    First, you’ll need ASI’s firmware updater, which can be found here.

    Second, you’ll need one of these files:

    Standard XY Controller Firmware

    Standard XYZ Controller Firmware

    Piezo Enabled XYZ Controller Firmware

    Installation of the Patch:

    – Install the Firmware5 updater on your computer.

    – Restart the computer and restart the ASI controller. This just makes sure no other program is controlling the stage.

    – Run the Updater5, and select the appropriate firmware files.

    – apply the update.

    – You should see a “firmware update complete” message when the update has finished.

    – Power-cycle the controller, and check that the system responds to joystick commands etc. Check that the firmware version on stage start-up reads “8.8f”. This indicates that the patch was successfully applied.

    – Run Elements – everything should work now, including the joystick.

    Thanks to Gary at ASI for working on this and for providing a solution so quickly! This customer support is why you are on my Blogroll as the “favorite stage”! – Austin

  • How to Set Large Icons in Elements

    This is useful for large screens that are using very high resolutions. Sometimes the icons are so small as to be hard to click and unreadable.

    Open Elements and select the View Menu, then Layout, then open the “Layout Manager”.

    ToolbarButton_001

    Next select the “Toolbar” Section on the Left (Step 1), then Select the “Large Icons” Checkbox on the right (Step 2). Finally to set this as the default option for all modes right-click the Toolbar icon and select “Apply to All”. Finally save the setting to a file “Step 3”. You should now have large icons!

    ToolbarButton_002

    – Austin

  • NIS Elements Stereo Zoom Settings

    The Auto-calibration feature in Elements (beginning in version 3.1) is a great thing to have. You simply choose the objective you are working with, the software knows what camera you are running, so the calibration is calculated for you when you add the objective list.

    While this is great for the compound scope systems out there, it’s not helpful for a variable-zooming stereo or macro system. Low and behold there is a nice feature in Elements to handle this, and here’s how it works:

    The feature is called “Zoom Configuration” and can be found under the “Devices” menu.

    elements location

    To use this feature you’ll need to have at least one objective declared under the Calibration menu ->objectives list.

    When you open the window you’ll see a configuration screen for the zoom optics. Configure as follows:

    zoom2

    Also – If you want the Zoom to appear in the live window you’ll need to check the “Zoom is located in the camera light path” checkbox.

    With this complete you can close the config window. You’ll see a new tool available on the toolbar which allows you to enter the zoom value before acquiring an image:

    zoom3

    Note that for this to work you’ll need to have selected the main objective as active before you’ll see a calibration value in your acquired image.

    This is an extremely useful tool and one I’m glad to see is available in Elements D up to AR!

    – Austin

  • Quick Image Merge in Elements

    If you want to merge multiple channels in Elements here is a quick solution:

    1. Make sure you have the channel tabs activated. Do this by clicking the Edit menu, then Options. Select the “Appearance” settings. Make sure the “Show Channel Tabs” box is checked.

    channel_merge_1

    2. open or acquire the first image. In the lower left corner of the image is the channel tab. Right click this tab. If you have not configured color configurations for your system (optical configurations) you will need to select properties, then change the channel name and color to suit the properties of that image.

    3. Right-Click again and select “Copy Selected Channel”.

    channel_merge_2

    4. Choose or acquire a second image. Again if needed on this new image set the channel properties (step 2). Place the cursor over the image and right-click. Select “Paste as New Channel”.

    channel_merge_3

    5. You should now have a single image with two channel tabs. You can now save this image to produce a composite. You can also repeat these steps and add more channels to the current merge. There is no realistic limit on the number of channels one image can have.

    channel_merge_4

    These instructions are available for print in a PDF file here.

    – Austin

  • Saving an image as you see it in Elements

    If there is one simple question I get during training sessions it’s “How do I save an image, so that I can open it using Photoshop or other programs, and have the image appear exactly as it does in Elements?”. The reasons for this are complicated. Suffice it to say if all you want is an image for display, and NOT for analysis, here’s what to do:

    1. Set the image Zoom to 100%. You can also do this by pressing the 1:1 button in the upper right corner of the image window.

    saveas_step1

    2. Under the Edit Menu, select “Create Full View Snapshot”.

    3. Save the resulting image.

    4. If you want to add a calibration mark to the image, make sure you set the position and size of the mark AFTER the image has been zoomed to 100%.

    Why is the 100% zoom required? Saving”As displayed” refers to basically capturing a screen shot and copying it to a new document. While this preserves all overlays, calibration marks, regions and thresholds, it also includes the current magnification. So if you create the snapshot when the image is at 50% zoom, you will end up with a new image at 1/2 of the resolution of the original image. Conversely you can create a full view snapshot of an image at 200%, and the system will double the resolution in the resulting image.

    In case you’d like to print this I’ve included a PDF version here.

    – Austin

  • Elements release for Lumenera cameras

    Here is the latest build for Elements if you are running a Lumenera camera. Follow the directions explicitly if you plan on updating or installing without a local rep available!

    Download

  • Dynamic Graph Output for Elements

    Happy New Year!

    Laura Sysko from Nikon sent us a How-To on outputting live graphs that can be included with a timelapse or other ND file. You can find the How To Here.

  • Elements 3.1 Released

    Nikon has released it’s major revision of Elements in version 3.1. (Build 587). There are several new features in this build and from what i’ve seen it’s quite stable. You can download the build here.

    – Austin

  • Copying Elements Settings for Multiple users

    After installing a new imaging system it’s common to receive a phone call or email that goes like this, “The IT guys stopped by today and added our computer to our comany/university network. Now all of our settings are lost!”. Why does this happen and what can be done?

    All settings for elements are stored on a per-user basis. When a different user logs in (i.e. the user assigned from a company network vs. the default user that is installed on the PC) the software expects that user to want his or her own settings. Thus no settings are copied over. In the majority of cases this should NOT be the use case for a user group. In my experience almst everyone would like to start with the “default settings” and then modify them to their needs. For now there isn’t a copy button available, so we need to manually copy the settings.

    Getting Started:

    Copying settings is actually a simple process if done correctly. A few notes on this:

    • When moving to a new domain or user, don’t delete the old user until the new user setup is working well for you!
    • Make sure to copy the backup files we generate to a common directory. For instance don’t save to the “desktop” when logged in as administrator, as non-admin accounts may not get access to the admin desktop, leaving you no way to snag the needed backup files. Instead copy the backup files into a folder like c:Elements_settings.

    Backing up:

    We need to back up 3 items: Program menu/docker layouts, optical configurations and macro settings.

    1. With the program running and all devices connected, click the “explore optical configurations” button.
    2. There are two backup buttons here. First click the Backup button that sits between the optical configs and the camera/scope settings. Save the file to back up the settings. Secondly click the backup button below the objective list. Name this backup_objectives.
    3. Once these files are backed up we can close the optical configuration window. Next we will back up the menu layouts and docker settings. To do this select the View menu, then Layout, then Layout Manager.
    4. In the layout manager we will export the current layout to an xml file. ***because all of these files are *.xml be sure to name them descriptively so you can figure out which file is for what backup later.
    5. Next we will check up on our macros. In some installations macros may be configured to run every time elements starts. In these cases when users are switched these “start-up macros” will need to be re-specified. To check if you are running any startup macros, go to the Macro menu, then select Options. In the window on the left-hand side you’ll see any macros that are set to load when elements starts, as well as whether those macros are activated as “start-up”. See the example below where I have one macro set as a start-up macro.
    6. Make sure to find where this macro file sits on the computer so that we can add it into the new user account later. This can be found by viewing the “full path” info below the white macro box.

    Copying Over

    With the backup complete we can log out of the current user and log in to our new user. Once logged in as the new user launch Elements.

    1. Open the optical configurations window. Click the Restore button below the objectives list and load the objectives backup file.
    2. Click the restore button next to the optical configurations and load the optical config backup file you saved earlier.
    3. Select the View menu, then layouts, then layout manager. Click the “Import Layouts” button and select the layout file backed up earlier.
    4. If you had any startup macros selected, click the Macro menu, then Options. Add any macros needed and set them to startup if required.
    5. Test the system to make sure the previous user account settings have been transferred successfully.

    Hopefully this guide will help users when needing to copy settings to new user accounts. There is nothing wrong with using the same three or four backup files and loading them into multiple user accounts as well! Please post here or email me if you’d like to see any additions or changes made to this entry.

    Austin Blanco

  • Elements Build 548 Released


    Yes this is a bit late. Things are busy these days!

    Elements B 548 can be found here if you need to download it. As usual back up all of your optical configurations and take screen shots of any filter configurations (i.e. if you are using sutter wheels) just to be safe.

    So far this build has been stable. Only one or two bugs discovered. The major addition I see is we can now run High Dynamic Range processing from within elements. I can see why this would be a major advantage for stereo systems, as well as fluorescent images where the signal differences can be large. Haven’t tried it yet but it looks great.

    Austin

  • What can programming macros do for me?

    I’ve been running into a lot of programming applications lately. The fun part about using the Elements (or other) programming system is the amount of utility and flexibility it can offer to end users. Most people think about programming in our industry only as it relates to image analytics. I wanted to point out some other things macros can do for you:

    Acquisition & Device Automation

    Do you have a stimulus device or method you want to trigger from your acquisition software? Almost every device on the market (FRAP illumniators, Profusion systems, heating systems, electrical signaling systems) can accept a command input from TTL. You can use Elements (or other software) to control the parallel port on your computer – giving you control of the device you already have. A macro can tell the device to start, stop, adjust a setting and can then record that command into elements (i.e. at what time point in a timelapse the command was issued).

    User convenience

    Are you always pressing the same buttons in software to control the microscope? You can use macros to assign keyboard keys to run special functions. For instance when you press the “0” key on the number pad you can make the microscope load a “DAPI” illumination setting and acquire an image.

    User interaction

    Do you only run a few experiments over and over? You may be working harder than needed by re-configuring your software to image with a specific protocol. You can use a macro to configure all of the settings you want in one operation, and then dial in specific changes you may want to adjust before acquisition.

    In general any button you press, number you enter or menu you click can automatically be performed inside of a macro. Keep this in mind any time you are repeatedly clicking on the same things and slowing down your work!!

    EXAMPLE DOWNLOAD
    You can find an example macro for use in Elements here. Open Elements, open the Macro menu and click Edit (or press F8) and copy the code from this page into the empty macro. Then just save and run it!

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