software for high content analysis

[Grzegorz Chodaczek]

*****
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.
*****

Dear confocal community,
I'm interested in a ready-to-use software for high content analysis of data
acquired on a Zeiss spinning disk Cell Observer with a motorized stage. I
was wondering whether any of you ever compared Columbus (Perkin Elmer) and
MetaXpress (Molecular Devices) or any other similar software? I would
appreciate any feedback about their pros and cons.

Best regards,
Grzegorz

[Douglas Richardson]

*****
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.
*****

Have you had a look at Cell Profiler? http://www.cellprofiler.org

-Doug

> On Jan 3, 2015, at 5:13 PM, Grzegorz Chodaczek <[hidden email]> wrote:
>
> *****
> 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.
> *****
>
> Dear confocal community,
> I'm interested in a ready-to-use software for high content analysis of data
> acquired on a Zeiss spinning disk Cell Observer with a motorized stage. I
> was wondering whether any of you ever compared Columbus (Perkin Elmer) and
> MetaXpress (Molecular Devices) or any other similar software? I would
> appreciate any feedback about their pros and cons.
>
> Best regards,
> Grzegorz

[Lit-Hsin Loo]

*****
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.
*****

Dear Grzegorz,

It depends on your throughput and the types of feature that you
want to measure from the images.

Columbus is based on OMERO (https://www.openmicroscopy.org),
which is freely available. Both of them are good for managing
and/or visualizing large numbers of images, but they only have
basic analysis capabilities. Also, the processing is done on the
server side, so you would need a very powerful server if the
workload is going to be heavy.  

You may also try cellXpress (http://www.cellxpress.org), which is
developed by us and currently one of the fastest software for
high-content image analysis. The cellXpress software can extract
more complex features, and has a convenient interface for
exporting the extracted features into Excel or the R environment
for further analysis or visualization.

Please feel free to PM me if you need help on using cellXpress.

Regards,
Lit-Hsin


On Sat, 3 Jan 2015 23:13:27 +0100, Grzegorz Chodaczek <[hidden email]>
wrote:

>*****
>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.
>*****
>
>Dear confocal community,
>I'm interested in a ready-to-use software for high content analysis of data
>acquired on a Zeiss spinning disk Cell Observer with a motorized stage. I
>was wondering whether any of you ever compared Columbus (Perkin Elmer) and
>MetaXpress (Molecular Devices) or any other similar software? I would
>appreciate any feedback about their pros and cons.
>
>Best regards,
>Grzegorz

[Avi Jacob]

*****
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.
*****

I second CellProfiler.
There is a learning curve like in any program, but for non-programers like
me, it was a godsend. I had tried the turn-key ScanR analysis package, and
found CP to be superior.

I now use it even for small data-sets and I highly recommend it.
They have good support too. When you try to build a pipeline yourself
(always start with the example ones) and get stuck, you can upload what you
made together with some example images to the forum, and they will usually
help you out - and if you are lucky they will even edit your pipeline.
Sometimes takes a couple days, but still, well worth it.

Avi


--




On Sun, Jan 4, 2015 at 12:36 AM, Doug Richardson <[hidden email]>
wrote:

> *****
> 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.
> *****
>
> Have you had a look at Cell Profiler? http://www.cellprofiler.org
>
> -Doug
>
>
>
> > On Jan 3, 2015, at 5:13 PM, Grzegorz Chodaczek <[hidden email]>
> wrote:
> >
> > *****
> > 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.
> > *****
> >
> > Dear confocal community,
> > I'm interested in a ready-to-use software for high content analysis of
> data
> > acquired on a Zeiss spinning disk Cell Observer with a motorized stage. I
> > was wondering whether any of you ever compared Columbus (Perkin Elmer)
> and
> > MetaXpress (Molecular Devices) or any other similar software? I would
> > appreciate any feedback about their pros and cons.
> >
> > Best regards,
> > Grzegorz
>

[mahogny]

*****
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.
*****

 

Hi Lit-Hsin!

I have never come a across the cellxpress package
before but it seems like a nice base package. However, it seems quite
limited in that it's not open source; After all, in any reasonable
complex project one will benefit from being able to modify and improve
the code. Any plans on resolving this in the future?

cheers,

Johan


2015-01-04 14:37 skrev Lit-Hsin Loo:

> *****
> To join, leave or
search the confocal microscopy listserv, go to:
>
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy [1]
> Post images
on http://www.imgur.com [2] and include the link in your posting.
>
*****
>
> Dear Grzegorz,
>
> It depends on your throughput and the
types of feature that you
> want to measure from the images.
>
>
Columbus is based on OMERO (https://www.openmicroscopy.org [3]),
> which
is freely available. Both of them are good for managing
> and/or
visualizing large numbers of images, but they only have
> basic
analysis capabilities. Also, the processing is done on the
> server
side, so you would need a very powerful server if the
> workload is
going to be heavy.
>
> You may also try cellXpress
(http://www.cellxpress.org [4]), which is
> developed by us and
currently one of the fastest software for
> high-content image
analysis. The cellXpress software can extract
> more complex features,
and has a convenient interface for
> exporting the extracted features
into Excel or the R environment
> for further analysis or
visualization.
>
> Please feel free to PM me if you need help on using
cellXpress.
>
> Regards,
> Lit-Hsin
>
> On Sat, 3 Jan 2015 23:13:27
+0100, Grzegorz Chodaczek <[hidden email]>
> wrote:
>
>> ***** To
join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy [1] Post images on
http://www.imgur.com [2] and include the link in your posting. *****
Dear confocal community, I'm interested in a ready-to-use software for
high content analysis of data acquired on a Zeiss spinning disk Cell
Observer with a motorized stage. I was wondering whether any of you ever
compared Columbus (Perkin Elmer) and MetaXpress (Molecular Devices) or
any other similar software? I would appreciate any feedback about their
pros and cons. Best regards, Grzegorz
 

Links:
------
[1]
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
[2]
http://www.imgur.com
[3] https://www.openmicroscopy.org
[4]
http://www.cellxpress.org