Tracking Cell Division in 3D/4D
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Nowell, Cameron |
Tracking Cell Division in 3D/4D
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Search the CONFOCAL archive at
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Hi List, Does anyone out there have any experience in
tracking cell division in 3D? We want to be able to track the resulting
daughter cells of T-cell division over a period of time (usually about 24
hours). We do not need to be able to do it in a live context (ie during acquisition),
we just want to be able to analyse the movie after capture. Thanks Cam Cameron
Nowell
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Chris Tully |
Re: Tracking Cell Division in 3D/4D
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Search the CONFOCAL archive at
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Cameron,
Semi-commercial response. Although I am not currently associated with Media Cybernetics, I have worked for them in the past. I have also been using and/or selling their software for the last 15 years. Image-Pro Plus by Media Cybernetics has an add-on module called 3D-Constructor which was specifically designed for rendering objects in 3D and tracking them in 4D. Image-Pro Plus will open 3D data sets from most sources (Leica, Nikon, Olympus and Zeiss confocal software, MetaMorph .stk, and multiple TIFF), and import the calibration and location data saved by the original software. There are even macros available to take a set of single frame images and turn them into a "Regular" set that Image-Pro's tools such as 3D-Constructor will recognize. If the acquisition times have been recorded for each frame of the data set, 3D-Constructor will automatically treat the data set as a 4D set and from there tracking is a "simple" matter of identifying your objects in each time point. Contact Media Cybernetics for more information (http://www.mediacy.com). Chris Tully Image Processing and Analysis Specialist 240-888-1021 [hidden email] On Tue, Apr 15, 2008 at 12:56 AM, Nowell, Cameron <[hidden email]> wrote: Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal -- Chris Tully Microscopy and Image Analysis Expert [hidden email] 240-888-1021 http://www.linkedin.com/in/christully |
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Badri Roysam |
Re: Tracking Cell Division in 3D/4D
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In reply to this post by Nowell, Cameron
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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear Cameron, My group has experience with this. Let us communicate offline. Badri Roysam Professor, Department of Electrical, Computer and Systems Engineering Associate Director, NSF Center for Subsurface Sensing & Imaging Systems (CenSSIS ERC) Rensselaer Polytechnic Institute 110 8th Street, Troy, New York 12180-3590. Office(JEC 7010): 518-276-8067, Lab(JEC 6308): 518-276-8207, Fax: 518-276-8715 Email: [hidden email], Web: http://www.ecse.rpi.edu/~roysam ----- Original Message ----- From: Nowell, Cameron [mailto:[hidden email]] To: [hidden email] Subject: Tracking Cell Division in 3D/4D > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Hi List, > > Does anyone out there have any experience in tracking cell > division in 3D? We want to be able to track the resulting daughter cells > of T-cell division over a period of time (usually about 24 hours). We do > not need to be able to do it in a live context (ie during acquisition), > we just want to be able to analyse the movie after capture. > > > > > > Thanks > > > > > > Cam > > > > > > > > > > > > Cameron Nowell > Microscopy Research and Imaging Facility > Cell Cycle and Development > Peter MacCallum Cancer Centre > 7 St Andrews Place > East Melbourne, 3002 > Victoria AUSTRALIA > > Phone: +61396563759 > Fax: +61396561411 > Mobile: +61422882700 > > > > > > > > This email (including any attachments) may contain > confidential and/or legally privileged information and is > intended only to be read or used by the addressee. If you > are not the intended addressee, any use, distribution, > disclosure or copying of this email is strictly > prohibited. > Confidentiality and legal privilege attached to this email > (including any attachments) are not waived or lost by > reason of its mistaken delivery to you. > If you have received this email in error, please delete it > and notify us immediately by telephone or email. Peter > MacCallum Cancer Centre provides no guarantee that this > transmission is free of virus or that it has not been > intercepted or altered and will not be liable for any delay > in its receipt. > |
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Nowell, Cameron |
Re: Tracking Cell Division in 3D/4D
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In reply to this post by Chris Tully
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Hi Everyone,
As is always the way with these things, now i have had a bit more of a think
about it i have some more information to add to my request. With the tracking
we want to be able to track a field of cells. If one of the cells divide we
want to be able to track the resulting daughter cells. I have used imaris in
the past but i don’t remember it having the capacity to recognise a cell has
divided and set up individual traces for the resulting daughter cells. Can
imaris (or any of the other software products mentioned by others) do this
specific function? And if so how reliable are they at doing it. Thanks Cam Cameron Nowell This email (including any attachments) may
contain
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Julio Vazquez |
Re: Tracking Cell Division in 3D/4D
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Search the CONFOCAL archive at
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Cameron, Don't think I have a real answer for you, but I want to say this: Some of the available imaging software can do amazing things, but sometimes you need to ask yourself whether you might just get the same information the old-fashioned way, i.e. by just looking at the images yourself. Imaris (and similar software) is certainly very good at identifying and tracking large numbers of objects over time, connecting the objects (based generally on intensity and shape similarities) to generate tracks, and extract numerical data such as velocity, etc... In your case though, I think what you need to do is to set your time lapse by using a reasonable time interval between your time-points, based on how much your cells move, change shape, or how fast they divide. For instance, I did such experiments to see meiosis in male flies (a 20-30 minute event happening within a 12-16 hour window). I first collected images every 15 minutes for 12-16 hours, and examined a number of time lapse movies. Then, when I was able to recognize cells that were about to divide and could narrow down my time window to a few hours, I would collect images every five minutes. This allowed me to capture individual meiosis events. In those conditions, you can "see" pretty much what is happening, and then measure whatever parameters are important for your experiment. I could have tried to have it done by software, but I would probably have made my life ten times harder. If you want to analyze hundreds of mitotic events, it might be worth the time and effort to investigate software solutions. If you want to analyze a few dozen or so events, I probably wouldn't bother trying to get it all automated... you can probably do that ivery easily by just looking at the movies, provided you use a reasonable time interval for your movies. If you can't track the cells by eye, chances are the software will struggle too... You can probably use something as simple as ImageJ to mark the dividing cells (and their daughters) and generate the tracks in projections of your time lapse series (we had good results with the track 3-D objects plugin, and there may be others... just look them up at the imagej web site), or you can segment your images with imagej, extract the position of the cells, such as center of mass or geometric center, and import your coordinates into Excel or similar package and do all the math in there. In any event, if you want to use software for this type of work, you need to first define very specifically what is is that you want to do, because you will have to "explain" it to the software... Then, I would recommend you start with the simplest possible approach (such as with ImageJ). Either that works, and you are done, or you find limitations, in which case you will know more precisely what to look for... If you do have Imaris already, they probably have a webinar in their archives that explains how to do the tracking, so you may also want to go and have a look at that... (check www.bitplane.com to find out). -- Julio Vazquez Fred Hutchinson Cancer Research Center Seattle, WA 98109-1024 Tel: Office: 206-667-1215/ Lab: 206-667-4205 FAX: 206-667-6845 -------------------------------------------------- This message is confidential, intended only for the named recipient(s) and may contain information that is privileged or exempt from disclosure under applicable law. If you are not the intended recipient(s), you are notified that the dissemination, distribution or copying of this information is strictly prohibited. If you received this message in error, please notify the sender then delete this message. On Apr 15, 2008, at 3:56 PM, Nowell, Cameron wrote: Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal |
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Chris Tully |
Re: Tracking Cell Division in 3D/4D
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In reply to this post by Nowell, Cameron
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Cameron,
Image-Pro Plus' 3D Constructor plug-in that I mentioned earlier in this conversation would not be able to do that out of the box. However, it is well supported by Image-Pro's built-in macro language which would allow you to develop a macro that would check each track for changes that indicate a split and then establish new tracks for each daughter cell. If you would like to try this out, please contact me directly using my email address ([hidden email]), and I will be more than happy to help you. -- Chris Tully Microscopy and Image Analysis Expert [hidden email] 240-888-1021 http://www.linkedin.com/in/christully On Tue, Apr 15, 2008 at 6:56 PM, Nowell, Cameron <[hidden email]> wrote:
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Michael Weber-4 |
Re: Tracking Cell Division in 3D/4D
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In reply to this post by Nowell, Cameron
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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hello Cam, yes, Imaris is able to split tracks and follow daughter cells - also vice versa. How well this works depends mainly on your dataset. With a rather high temporal resolution (cells move less than their diameter between two frames) and well defined cells (spatial resolution, signal-to-background) it shouldn't be a problem. If you would like to go this way, I recommend to directly ask your local Bitplane representative to give you an introduction. Michael > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Hi Everyone, > > As is always the way with these things, now > i have had a bit more of a think about it i have some more information > to add to my request. With the tracking we want to be able to track a > field of cells. If one of the cells divide we want to be able to track > the resulting daughter cells. I have used imaris in the past but i don't > remember it having the capacity to recognise a cell has divided and set > up individual traces for the resulting daughter cells. Can imaris (or > any of the other software products mentioned by others) do this specific > function? And if so how reliable are they at doing it. > > > > Thanks > > > > > > Cam > > > > > > > > > > > > Cameron Nowell > Microscopy Research and Imaging Facility > Cell Cycle and Development > Peter MacCallum Cancer Centre > 7 St Andrews Place > East Melbourne, 3002 > Victoria AUSTRALIA > > Phone: +61396563759 > Fax: +61396561411 > Mobile: +61422882700 > > > > > > This email (including any attachments) may contain > confidential and/or legally privileged information and is > intended only to be read or used by the addressee. If you > are not the intended addressee, any use, distribution, > disclosure or copying of this email is strictly > prohibited. > Confidentiality and legal privilege attached to this email > (including any attachments) are not waived or lost by > reason of its mistaken delivery to you. > If you have received this email in error, please delete it > and notify us immediately by telephone or email. Peter > MacCallum Cancer Centre provides no guarantee that this > transmission is free of virus or that it has not been > intercepted or altered and will not be liable for any delay > in its receipt. > > > > > -- > Chris Tully > Microscopy and Image Analysis Expert > [hidden email] > 240-888-1021 > http://www.linkedin.com/in/christully > > > > This email (including any attachments) may contain > confidential and/or legally privileged information and is > intended only to be read or used by the addressee. If you > are not the intended addressee, any use, distribution, > disclosure or copying of this email is strictly > prohibited. > Confidentiality and legal privilege attached to this email > (including any attachments) are not waived or lost by > reason of its mistaken delivery to you. > If you have received this email in error, please delete it > and notify us immediately by telephone or email. Peter > MacCallum Cancer Centre provides no guarantee that this > transmission is free of virus or that it has not been > intercepted or altered and will not be liable for any delay > in its receipt. |
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