Introduction To Image Analysis Using Imaris August 2014 | Bitplane

Introduction to Image Analysis using Imaris

Kevin Frischmann - August 2014

In this webinar, we discussed the basic concepts of image analysis (3D rendering modes, object detection with surfaces & spots and getting quantitative information from the image).

There is also a Q&A session recorded, where our Imaris Application Specialists provided you with lots of tips and solutions to your specific data types, and answered your questions demonstrating live in Imaris.

Please view the recording below and browse through the Q&A session at the bottom of the page, where you will also find links to the recorded versions of the Q&A sessions.

Q & A from the above webinar:

You can choose to watch the Q & A from Session One or the Q & A from Session Two, or for the full list of questions and answers please select the tab below.

Can I do a filament reconstruction and a surface reconstruction of the same neuron, and then link them somehow in order to extract precise volume and surface information per filament (essential for modelling neurons with non-circular cross-section)?

It is not possible to do this directly in Imaris, but it is possible to modify the “Split branch” XTension to split each filament into segments, which can then be used to tag different filaments with a unique intensity, which can then be used to correlate which filament segment matches a particular surface section.

Would Vantage work to summarize a batch of data?

Yes, it can be used in current Imaris version but will this functionality will be facilitated and expanded from Imaris 8 version.

What file extensions does Imaris currently support?

Imaris supports many many file formats: all major confocal formats including, CZI, LSM, LEI, LIF, OIB, OIF, ND2, Praire, BioRad, HCImage/SimplePCI CXD.

I have a collection of images that contain data from two separate channels and I would like to process them for statistical data using a program outside of Imaris. However, I need to input these channels separately into this statistical program so that I can compare the signals.  Is it possible to input a 2 channel image into Imaris and then export each channel separately as a TIFF?

Yes. Imaris has options to export to a .TIF images. Use either OME-TIF or "Tiff Adjustable File series" when you save the file from Imaris.

 The colors in the original Andor multi-tiff file are altered.  How do I open such a file with the original colors?

You can change the behaviour of Imaris  -->Preferences-->Loading and you can change where Imaris gets colors from, either "Default Colors" "File Colors" or "Emission Wavelength".

Is there a way to measure in the XYZ orthoview? Or do all measurements need to be done in the surpass mode?

It is possible to make simple distance measurements in the Slice view, but all other measurements are made in the Surpass View.

My lab uses IMARIS for neuroscience research, particularly dendritic spine analysis. When I build a surface for each spine type I get measurements such as diameter length etc for the entire spine. However, I'm interested in getting this type of data for the neck and head of the spine separately. Is there a why I can construct a surface for these separate properties of the spine?

If you use the FilamentTracer tool, you can get information about spines head and neck separately. The surfaces object does not have any specific information about that.

When you change a color and pick a red, is there any way to choose that same red for a different file?

There are two ways you can use the same color: (one) use a look up table and save the .pal file in the correct location in Imaris Install folder (look for "color tables" sub folder)  and (two) you can enter the same RGB information in the Base color section.. e.g. R : 0 ; G: 1  ; B: 0 .

How are you able to merge several 3D images to create 4D timelapse datasets?

If all 3D Time points are the same XYZ dimensions and bit depth, use Edit-->Add Time points and you can assemble multiple images into a larger file

Are you able to rotate a region of interest within an image or are you only able to rotate an entire image?

Only the entire image can be rotated - not individual sub sections. 

If I have a z-series with several neurons and I would like to work only with one neuron, how can I mask the other ones?

You can use the Region of Interest option in the Filament Creation wizard to only select a single Neuron.

Can Imaris be used for ROI intensity measurement from brightfield 2D images (time-lapse imaging)?

To set a ROI in a 2D time series, you have to manually create the ROI, using a contour surface, duplicate to all time points, and then you can get the information from all time points! :)

If there is drift in a time series and you are trying to track spots, how do you correct for that?

Once the tracking is finished - it is easy to run a drift correction (function in Imaris).

Are 8-bit or 16-bit images preferred or does it not matter?

The more bits available the more sensitive your analysis will be to changes in intensity

Is there a way to determine overlap between spheres created in different channels?

Yes, you need to use "Spots Colocalize" XT within Imaris

In a 4D file, I need to measure the multiple spots' contact time of two cell groups. How can I do?

Imaris does not have a specific contact measurement, but it is possible to use a “Distance transform” XT on one set of spots - and then this will create a new channel of information in the image, and then look in the other set of spots to see the distance as intensity. So if you look for objects whose minimum intensity is "zero" you know that those objects are in contact with the first set of objects. 

I understand that Sholl analysis can be found in the statistics tab after creating the filament. Is there any way that the radius may be manipulated?

The radius is adjustable in the  Preferences-->Advanced-->filament-->Sholl radius.

How do you measure distance between spots?

There are several methods.  Either you can do a manual measurement using the Measurement Point objects, or you can use one of our XT functions, like Spots close to Spots, or Spots Colocalize, or Distance transform, depending on what specific measurements you are interested in.

Does Imaris run on Mac OSX? Linux? Which versions of Windows?

Imaris runs on Windows Vista / Win7 / Win 8.0 / 8.1, as well as OSX 10.6 and later. With the upcoming 8.0 release we will drop support for 32-bit Windows.

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