Re: Measurement of cavity/void volume in Imaris?

[Sylvie Le Guyader]

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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



@@@@@@@@@@@@@@@@@@@@@@@@

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: [phone]

LCI room 1: [phone]

LCI room 2: [phone]

mobile: [phone]





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

> From: Nate Jowett [mailto:[hidden email]]

> Sent: 07 November 2013 19:15

> To: [hidden email]; 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

>

[Erik von Stedingk]

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Hi!
(Obviously partial as I work for Bitplane)

I cannot see the data set from my phone, but I wanted to point out that I recently had an interesting solution with a sample where we couldn't use the membrane stain algorithm for tracking: we made a mask around the volume, encompassing the whole tissue, then we set the outside to a max value (in this case 255). Then we inverted it, turning the 255 to zero. And lo: the cells were defined by an internal "cytosolic" signal which dropped off at the PMs. Not perfect close to the borders of the mask but solved this particular problem. Maybe the same tactic could help here?

Best regards
Erik

(sent from mobile)

> 29 nov 2013 kl. 16:40 skrev Sylvie Le Guyader <[hidden email]>:
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> 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
>
>
>
> @@@@@@@@@@@@@@@@@@@@@@@@
>
> 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: [phone]
>
> LCI room 1: [phone]
>
> LCI room 2: [phone]
>
> mobile: [phone]
>
>
>
>
>
>> -----Original Message-----
>
>> From: Nate Jowett [mailto:[hidden email]]
>
>> Sent: 07 November 2013 19:15
>
>> To: [hidden email]; 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
>
>>