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Combining z stack with timelapse

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Julia Edgar

Combining z stack with timelapse

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Thanks Timothy.
I have now changed the subject header.....
I'm imaging the movement of organelles (~ 50 nm diameter) within a structure with a depth of around 2-3 um, hence the reason I need to combine timelapse (1 frame every 10 seconds) with z stack.
Best wishes

Julia

As a rule I try to keep the analysis and the presentation as straightforward as possible by reducing dimensions and cropping. If I have to include depth, time, and color then I usually generate a volume projection and have it rotate slowly while advancing in time. Most proprietary scope software is good at this, though you often have to pay a substantial extra license for the volume/movie option. ImageJ/Fiji is not ideal but I found Fluorender and Vaa3D to be good free alternatives.

Bear in mind that volume rendering involves a lot of semi-arbitrary and nonlinear transformations. So that sort of display is best if it can supplement quantitative analysis rather than stand on its own.

Best,

T

Timothy Feinstein, Ph.D.

> On May 25, 2019, at 3:49 AM, Julia Edgar <[hidden email]> wrote:
>
> *****
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> Post images on https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.imgur.com&data=02%7C01%7Ctnf8%40PITT.EDU%7C37217e5d7f2d4da10e6d08d6e0e5752b%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C636943673473526194&sdata=kRiTixuJ4TypED3sqISbUldlF5gWId2UiBxpAJwsdaU%3D&reserved=0 and include the link in your posting.
> *****
>
> Dear All
> A very naive question I know...
>
> How do you display time-lapse combined with confocal z stack? Flatten the z stack and play the time-lapse movie of the flattened (maximum intensity projection?) images?
>
> If so, how do you generate the movie using Zen software and/or Fiji?
>
> Many thanks in advance.
> Julia
>
> Get Outlook for iOS<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Faka.ms%2Fo0ukef&data=02%7C01%7Ctnf8%40PITT.EDU%7C37217e5d7f2d4da10e6d08d6e0e5752b%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C636943673473526194&sdata=LGBXuDrGU6PccKel94UFmyDp3dYKyREbCb1ZV0neyyA%3D&reserved=0>
>
> ________________________________
> From: Confocal Microscopy List <[hidden email]> on behalf of Ralf Palmisano <[hidden email]>
> Sent: Saturday, May 25, 2019 1:47 am
> To: [hidden email]
> Subject: Re: SSD-RAID for new wide-field microscopy system
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
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> Post images on https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.imgur.com&data=02%7C01%7Ctnf8%40PITT.EDU%7C37217e5d7f2d4da10e6d08d6e0e5752b%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C636943673473526194&sdata=kRiTixuJ4TypED3sqISbUldlF5gWId2UiBxpAJwsdaU%3D&reserved=0 and include the link in your posting.
> *****
>
> Hi Mirco,
>
> I am literally signing everything Nuno Mureno wrote. In addition whoever is the manufatcurer. I consider it bad advise to invest in an 11 GB graphics card and even worse to call 6.000$ for a 2 TB SSD extension. That is just playing foul or they have no clue about what they are selling and why...
>
> My pennie in here
>
> Ralph
>
>> Am 23/05/2019 um 14:57 schrieb Nuno Moreno:
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
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>> Post images on https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.imgur.com&data=02%7C01%7Ctnf8%40PITT.EDU%7C37217e5d7f2d4da10e6d08d6e0e5752b%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C636943673473526194&sdata=kRiTixuJ4TypED3sqISbUldlF5gWId2UiBxpAJwsdaU%3D&reserved=0 and include the link in your posting.
>> *****
>>
>> Hi Mirco
>>
>> Honestly I see no reason to have so much memory and such a high spec graphics card for an acquisition computer. Regarding the HDs, I would keep the 2TB and add extra space non SSD. Then just automate data flow from the fast to the slow drive. 2TB extra for 6000$ is just too much and might be too short anyway.
>>
>> Just my 2 cents
>> \N
>>
>>
>>
>>> On 23 May 2019, at 14:38, Mirco Martino <[hidden email]> wrote:
>>>
>>> *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>> https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.umn.edu%2Fcgi-bin%2Fwa%3FA0%3Dconfocalmicroscopy&data=02%7C01%7Ctnf8%40PITT.EDU%7C37217e5d7f2d4da10e6d08d6e0e5752b%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C636943673473536187&sdata=466LSBiLMjW2ge9y2Lhu3yISXXttR3R%2FHQmK4micXeQ%3D&reserved=0
>>> Post images on https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.imgur.com&data=02%7C01%7Ctnf8%40PITT.EDU%7C37217e5d7f2d4da10e6d08d6e0e5752b%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C636943673473536187&sdata=47wjiIRXYriXmXI8TUK4m0Y74zV7uwKkek2qmQHD000%3D&reserved=0 and include the link in your posting.
>>> *****
>>>
>>> Hi all,
>>>
>>> we are buying a new fluorescent microscope wide-field system. The system include a workstation with 64GB DDR4 RAM, 11GB of graphic card, 512 gb of memory and SSD-RAID of 2TB. There is an option to increase the SSD-RAID to 4TB for about 6000$ extra. The system will be use for both fixed materiel imaging and for live-imaging with time-laps, z-stack, tiling and multi-fluorophores experiments. I was wondering if it is worth to invest those extra money for this option or not. This will be the first time we will have time-laps experiments, so I don't know what to expect as pictures size.
>>>
>>> What do you think?
>>>
>>> Thanks in advance for your comments and opinions!
>>>
> --
> Ralf Palmisano
> Head - Optical Imaging Centre Erlangen
>
> Fellow Royal Microscopical Society
> Member Royal Society of Medicine
>
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Ann-W

Re: Combining z stack with timelapse

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Post images on http://www.imgur.com and include the link in your posting.
*****

Hi Julia

Our facility is open and we aren't too far from Glasgow. If you would like to have a chat about what you are trying to do and how best to do it please send me a PM. We have experience of most of these sort of applications.

Best

Ann

Dr Ann Wheeler
Advanced Imaging Resource, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU
Working Pattern. Mon, Tues 9.30am - 2.30pm, Weds 9.30am - 4.30pm, Thurs 9.30am - 12.30pm
E: [hidden email]
T: 0131 651 8665
W: http://www.igmm.ac.uk/imaging.htm

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Julia Edgar
Sent: 25 May 2019 14:52
To: [hidden email]
Subject: Combining z stack with timelapse

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Thanks Timothy.
I have now changed the subject header.....
I'm imaging the movement of organelles (~ 50 nm diameter) within a structure with a depth of around 2-3 um, hence the reason I need to combine timelapse (1 frame every 10 seconds) with z stack.
Best wishes

Julia

As a rule I try to keep the analysis and the presentation as straightforward as possible by reducing dimensions and cropping. If I have to include depth, time, and color then I usually generate a volume projection and have it rotate slowly while advancing in time. Most proprietary scope software is good at this, though you often have to pay a substantial extra license for the volume/movie option. ImageJ/Fiji is not ideal but I found Fluorender and Vaa3D to be good free alternatives.

Bear in mind that volume rendering involves a lot of semi-arbitrary and nonlinear transformations. So that sort of display is best if it can supplement quantitative analysis rather than stand on its own.

Best,

T

Timothy Feinstein, Ph.D.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

Ann Wheeler
Head of Advanced Imaging Facility
Institute of Genetics and Molecular Medicine
University of Edinburgh
United Kingdom