Category: NIS Elements BR

  • 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

     

  • 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 canĀ  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

  • 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

  • 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

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