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Hi Nate



I was just checking the Imaris videos right now and I bumped into this one<http://www.bitplane.com/learning/masking-properties-of-imaris-tutorial?utm_medium=email&utm_campaign=Bitplane%20Newsletter%20November&utm_content=Bitplane%20Newsletter%20November+CID_d1e23c1fb6de0a77471d4a37a771960d&utm_source=Email%20marketing%20software&utm_term=Click%20here%20to%20read%20the%20How%20To> that might help you in your analysis. You can create a surface completely manually then use this as a mask to analyse the data only inside the surface.



Med vänlig hälsning / Best regards



Sylvie



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Sylvie Le Guyader

Live Cell Imaging Unit

Dept of Biosciences and Nutrition

Karolinska Institutet

Hälsovägen 7

Novum, G lift, floor 6

14157 Huddinge

Sweden

office: +46 (0) 8 5248 1107

LCI room 1: +46 (0) 8 5248 1172

LCI room 2: +46 (0) 8 5248 3542

mobile: +46 (0) 73 733 5008





> -----Original Message-----

> From: Nate Jowett [mailto:[log in to unmask]]

> Sent: 07 November 2013 19:15

> To: [log in to unmask]; Sylvie Le Guyader

> Cc: Nate Jowett

> Subject: Re: Measurement of cavity/void volume in Imaris?

>

> Hi Sylvie

>

> Thank you for your suggestion - it is excellent, but I do not believe it is

> workable with my data set.   The problem is that the tissue is only surface

> stained (with a terrible signal/noise ratio) so the surface creation inside the

> rectangular ROI also encompasses volume on the other sides (deep and lateral) of

> the ablation cavity.

>

> I have attached a video here of my data set - you can clearly see what the issue is.

>

> The ability to define a free-form ROI would solve this issue, but I do not believe

> this is possible in Imaris.  Perhaps I could try applying clipping masks, but again I

> would need to define a non-linear surface to clip, as the ablation cavity walls are

> conical in shape.

>

> I will attempt the suggestion to negatize the image with the -1 function, but I think I

> will run into the same issue.

>

> Any more suggestions would be greatly appreciated!

>

> Thanks

>

> Nate

>