Octane plugin in FIJI

[Colin Rickman-3]

Hi

I'm trying to install the Octane plugin in FIJI. I've followed the instructions on the site and installed Apache commons math library but can't get it to show up in the plugins drop down menu. Does anybody know what I have done wrong?

Thanks

Colin
Dr Colin Rickman
Institute of Biological Chemistry, Biophysics and Bioengineering
School of Engineering and Physical Sciences
Heriot-Watt University
Edinburgh
EH14 4AS

Tel: [phone] (Office)

http://www.ib3.eps.hw.ac.uk
http://lifescienceinterface.hw.ac.uk





--
Heriot-Watt University is a Scottish charity
registered under charity number SC000278.

Heriot-Watt University is the Sunday Times
Scottish University of the Year 2011-2012

[ctrueden]

Hi Colin,

I'm trying to install the Octane plugin in FIJI. I've followed the
> instructions on the site and installed Apache commons math library but
> can't get it to show up in the plugins drop down menu. Does anybody know
> what I have done wrong?
>

Are you sure you downloaded octane-1.1_.jar and put that in your Fiji
plugins folder as well?

I was able to get Octane to appear in the Plugins menu by doing so.

However, there is a problem. Octane requires commons math 2.2, but Fiji
ships with commons math 3.0, which does not provide backwards compatibility
with version 2.2. So you will likely have trouble running the Octane
plugins (give it a try, but if you receive a commons-math-related error
message, this is probably why).

-Curtis


On Tue, Jan 24, 2012 at 6:58 AM, Colin Rickman <[hidden email]> wrote:

> Hi
>
> I'm trying to install the Octane plugin in FIJI. I've followed the
> instructions on the site and installed Apache commons math library but
> can't get it to show up in the plugins drop down menu. Does anybody know
> what I have done wrong?
>
> Thanks
>
> Colin
> Dr Colin Rickman
> Institute of Biological Chemistry, Biophysics and Bioengineering
> School of Engineering and Physical Sciences
> Heriot-Watt University
> Edinburgh
> EH14 4AS
>
> Tel: [phone] (Office)
>
> http://www.ib3.eps.hw.ac.uk
> http://lifescienceinterface.hw.ac.uk
>
>
>
>
>
> --
> Heriot-Watt University is a Scottish charity
> registered under charity number SC000278.
>
> Heriot-Watt University is the Sunday Times
> Scottish University of the Year 2011-2012
>

[dscho]

[Resending since the ImageJ list rejects attachments of type
'APPLICATION/JAVA-ARCHIVE' which I am sure nobody wants to send to the
ImageJ list]

Hi Colin, Curtis and Ji Yu,

On Tue, 24 Jan 2012, Curtis Rueden wrote:

> Hi Colin,
>
> > I'm trying to install the Octane plugin in FIJI. I've followed the
> > instructions on the site and installed Apache commons math library but
> > can't get it to show up in the plugins drop down menu. Does anybody
> > know what I have done wrong?
>
> Are you sure you downloaded octane-1.1_.jar and put that in your Fiji
> plugins folder as well?
>
> I was able to get Octane to appear in the Plugins menu by doing so.
>
> However, there is a problem. Octane requires commons math 2.2, but Fiji
> ships with commons math 3.0, which does not provide backwards
> compatibility with version 2.2. So you will likely have trouble running
> the Octane plugins (give it a try, but if you receive a
> commons-math-related error message, this is probably why).

Since Curtis notified me of the problem, I took a stab at it.
Unfortunately, it seems that the Github repository of Octane no longer
exists, indeed the account does not exist any longer! Ji Yu, what is the
reason for this?

Anyway, I managed to get a version compiling with commons-math 3.0, but I
seriously lack the time to test it (although I verified that
Plugins>Octane>Options shows the dialog I expected it would). Colin, feel
free to contact me (on or off list, even if I prefer on list unless it
becomes totally technical) if it does not work for you.

Please find the compiled plugin at http://fiji.sc/snaps/Octane_.jar; the
changes required to compile it in Fiji can be seen here:
http://fiji.sc/cgi-bin/gitweb.cgi?p=fiji.git;a=commitdiff;h=a75197f64ed86474fe74fbc2547785a2d9a51863

Ji Yu, feel free to pick up my fixes should you reinstate the source code
repository again.

Ciao,
Johannes

[Colin Rickman-3]

Hi

Thanks for all your help. The new compiled version from Johannes seems to be running ok.

Colin
Dr Colin Rickman
Institute of Biological Chemistry, Biophysics and Bioengineering
School of Engineering and Physical Sciences
Heriot-Watt University
Edinburgh
EH14 4AS

Tel: [phone] (Office)

http://www.ib3.eps.hw.ac.uk
http://lifescienceinterface.hw.ac.uk



On 24 Jan 2012, at 19:43, Johannes Schindelin wrote:




--
Heriot-Watt University is a Scottish charity
registered under charity number SC000278.

Heriot-Watt University is the Sunday Times
Scottish University of the Year 2011-2012

[dscho]

Hi Colin,

On Wed, 25 Jan 2012, Colin Rickman wrote:

> Thanks for all your help. The new compiled version from Johannes seems
> to be running ok.

Great news, thank you!

Ciao,
Johannes

[Beling, Bill (MPAU)]

 Information is good, to much is a problem.  Please release me from the list.

Thanks

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