This is a calculator that will look at an ND experiment and tell you how large the resulting ND file will be. This is approximate and keep in mind if you are using the “save to TIFF” function the total size will likely be larger, due to the metadata saved per image in the tiff format.
- I’ve added this to the free macros list also.
Austin
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”.
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!
- Austin
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.
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:
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:
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
If you are running micro manager and need to control a device via TTL or voltage, there is a nice driver written for umanager along with an inexpensive A/D card. The Card I used for a recent project was the Velleman K-8061. I’ve written up a simple how-to on connecting the board to a windows PC and getting umanager to run it.
Setup instructions for the Velleman Board and uManager 1.3
uManager Wiki on the K-8061 board
-Austin
Thanks to everyone who attended my first course on image processing (and acquisition as it turns out). As promised here are some links:
- MBF Tools for ImageJ. This is a suite of processing and analysis tools, provided by the McMaster Biophotonics Facility, which can be used for, among other things, splitting apart pigment based IHC specimen images.
***One of the course attendees asked how to merge multiple channels, without using primary color (RGB) values. For instance one may want to select “Red, Cyan and Green”. This function is available using the MBF Tools function found under Plug-Ins, then under the “Colour Functions” and finally using the “Colour Merge” command.
- This tool only merges two channels. It is possible to run this multiple times, so a merge can have a third channel added to it, and so-on.
- LOCI Formats Importer/Exporter is a tool which can be used to read and write many file types. It can also import metadata from many of the proprietary file types used today.
- I was not able to find a dynamic and interactive particle counting plugin for ImageJ, however when you have produced a count by selecting “Analyze particles” you can select the “Distribution” command from the Analyze menu to produce histogram distributions for every measurement type selected.
Please contact me if you have any other items you’d like me to cover. Thanks again!
- Austin
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.
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”.
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”.
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.
These instructions are available for print in a PDF file here.
- Austin
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.
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
If you are enrolled for the Bio-X Image Processing and Analysis Workshop, I want to make sure you get the most from the course. To that end:
- Austin
When using the “Wellplate2″ Macro with NIS AR you may have noticed a small but important limitation: Once you’ve loaded your specified sites into the 6D experiment, you can no longer make adjustments to the scope PFS offset. This means that for each experiment you run you either need the offset to stay the same, or you need to reload the sites into the ND window. I’ve made a simple workaround for this.
By running a small macro we can turn on the PFS, move the offset to a pre-determined value (that is defined by the user before running the experiment) and then disable the PFS while moving to the next plate.Here’s a walk through on how to set the macro up and on a description of the problem:
Problem: Note that the PFS values are off while I add sites to the experiment:
When I now enable to PFS the default values (0) are active. While this is not the case if I send the sites with the PFS on, I still cannot alter the sites in future experiments.
So when you install the macro (which can be found at the end of this post) you’ll need to set the macro up so that it runs each time elements loads. To do this go to the options menu and add the macro. Then set it as a “Start-Up” macro as shown here -
With that done we can restart elements and this will run the macro code.
Next we add the calls needed to the experiment to operate the macro. Your XY experiment window should look as follows in the “Advanced” section:
Finally we need to enter the value for the PFS offset. To do this select Macro menu, then Command, and choose the “Interpreted” command group. You should see three entries at minimum, one called “PFS_define_offset(). Run this command and enter the offset value you need for your experiment.
That’s it! Now each time your stage is moved to a new position this macro will override the PFS entered into the XY list and will set the value you specified in the step above. For ease of use the command above can be added to a menu entry or a button (using the layouts) if needed.
You can find the macro HERE.
-Austin
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!
