Hello everybody,
I'm a first year PhD student on evolutionary biology. As I work on the karyotyping of a species of earthworm, I would like to know if there is a software designed for this, cause sometimes I see chromosomes on my lames but impossible to count them.
Thanks alot.
As a cytologist first and foremost is to standardized the hypotonic solution treatment and take the good well spread photographs of your metaphase plates, then you can cut in photosoft, or can used Morpho J, or Levan et soft. I know a bit about cytology if you want I could be some helps
A bit more information would be helpful- What is the goal of the karyotyping you are doing, and how are you karytyping? FISH/GISH, giemsa banding, or a general stain such as DAPI or carmine? Assisted with flow cytometry? My experiences from plants and some animals is that good technique by hand is key but challenging (very common to have overlapping and difficult to count chromosomes), and that software is limited without good discrimination among chromosomes by probes. Experimentation with methods to get good condensed chromosomes and technique can be a fair bit of work. If ywhat you need is broad variation in genome size/ploidy estimation, flow cytometry may be an alternative.
As a cytologist first and foremost is to standardized the hypotonic solution treatment and take the good well spread photographs of your metaphase plates, then you can cut in photosoft, or can used Morpho J, or Levan et soft. I know a bit about cytology if you want I could be some helps
I agree with a previous answer, you need a well-spread metaphases to count the chromosomes in a right software. I work in animal cytology (mammals) and use LUCIA soft or Metapher soft. They are very similar.
Well the goal is to have the ploidy degree of this species as we have no information about and I use Giemsa binding. I have my lames and I see the chromosomes (however difficult to count as sometimes they are superposed or very little), so I think I have still a lot to do to have a nice protocole. Withall, I wanted to start some karyotyping with what I have. Thanks alot for your answers.
Applied Spectral Imaging (see Google) has a software that may fit your need.
may this can help you
http://www.tandfonline.com/doi/abs/10.1080/00087114.2014.998526?journalCode=tcar20#.VTbuYVWqqko
To access the full text version of the paper you can get it from the author's page in RG
At the moment try this
http://www.ri.com.my/#!gen---karyotyping--cytogenetics/cbc
I have worked with human chromosomes using Metasystems IKAROS software [am strong admirer of the same], and also software by Applied Imaging, another good one. With Computer Engineering department we have also made our own version for automation - once we capture good quality image with CCD camera attached to microscope - any software can help, as rightly said above, quality preparation is needed.
This could be cheaper software: VideoTest
http://www.videotest.ru/en/products/17
I am not aware of any software that can be used to analyse the karyotype automatically. It is feasible, however to analyse the karyotype by manually manipulated image-editing and optimization softwares. One important thing is that a good chromosome spread is necessary and secondly, good stainability will help karyotype analysis.
there are many a few commercial software programs that can perform karyotyping:
Leica Cytovision system:
http://www.leicabiosystems.com/pathology-imaging/cytogenetics/
metasystems:
http://www.metasystems.org/index.php/karyotyping
applied spectral imaging:
http://www.spectral-imaging.com/applications/cytogenetics/karyotyping
Non-specialized graphics-processing free software which could be useful also in such cases: 1) GIMP - http://www.gimp.org ; 2) ImageJ - http://imagej.nih.gov/ij/
Thanks Joseph for the information. I have already contacted Metasystems and received a brochure. Have you used all three of them, i.e. Leica biosystems, Metasystems and Spectral Imaging? I will like to know which one is most friendly and gives the best output.
i always suggest for this.
https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fwww.spectral-imaging.com%2Fapplications%2Fcytogenetics%2Fkaryotyping
I use the Image Pro Plus software for capturing images of the chromosomes but not for performing countings or the automatic karyotyping of chromosomes. This software can also make chromosome counts but it is possible and easier only when the chromosomes are standardized and very well spread without superposed. If you can not count because the number is very high I suggest you to make a sketch of chromosomes from photographs of good metaphase chromosomes in a paper or ultimately do it directly on the image on the computer screen with a pen marker. The main work is to obtain good preparations.
I am also looking same information. Thanks for the ifo i got on this platform.
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