Simple Neurite Tracer - Connecting existing branches

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Simple Neurite Tracer - Connecting existing branches

Volko Straub
Dear All,

I have used Simple Neurite Tracer to trace neuronal morphologies. During
the analysis of the traces, I realised that some of the lower order side
branches are not correctly connected to their parent branch (must have
forgotten to press the branch modifier keys during the tracing). Is
there a simple/convenient way to connect two existing branches within
Simple Neurite Tracer (I don't seem to be able to find that option), or
perhaps an option to edit the trace files created by Simple Neurite Tracer.
On a related note, I was wondering whether there is a simple way to
access the path parameters such as start and end coordinates and path
length from a macro. I know that I can export them as a csv file, but it
seems a bit clunky to first export them as a csv file and then read the
parameters from there.
Any ideas/suggestions would be very much appreciated.

Thanks,
Volko

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Re: Simple Neurite Tracer - Connecting existing branches

ctrueden
Hi Volko,

My lab does not use this plugin, so I do not know the answers to your
questions. I'm sorry to say that the Simple Neurite Tracer is largely
unmaintained now, since the original author left the ImageJ community. The
core Fiji team is able to review and accept suggested code changes proposed
by others, but we unfortunately do not have time to fix bugs ourselves.

If any developers in the community are familiar with the Simple Neurite
Tracer and want to adopt it, please post on the ImageJ Forum—that would be
most welcome indeed.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Thu, May 26, 2016 at 1:11 AM, Volko Straub <[hidden email]> wrote:

> Dear All,
>
> I have used Simple Neurite Tracer to trace neuronal morphologies. During
> the analysis of the traces, I realised that some of the lower order side
> branches are not correctly connected to their parent branch (must have
> forgotten to press the branch modifier keys during the tracing). Is there a
> simple/convenient way to connect two existing branches within Simple
> Neurite Tracer (I don't seem to be able to find that option), or perhaps an
> option to edit the trace files created by Simple Neurite Tracer.
> On a related note, I was wondering whether there is a simple way to access
> the path parameters such as start and end coordinates and path length from
> a macro. I know that I can export them as a csv file, but it seems a bit
> clunky to first export them as a csv file and then read the parameters from
> there.
> Any ideas/suggestions would be very much appreciated.
>
> Thanks,
> Volko
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Simple Neurite Tracer - Connecting existing branches

Volko Straub
Hi Curtis,

Thanks for the response. It is a bit of a shame that Simple Neurite
Tracer is not more actively maintained as I think that it does a great
job. Unfortunately, a lack of expertise, programming skills and time
prevents me from having a look at the actual code of the plugin (my
'programming' in ImageJ is restricted to writing Macros).
This is also the biggest hurdle for me at the moment as the commands
within the Simple Neurite Tracer plugin are not macro recordable, which
means that I can open the Simple Neurite Tracer from a macro, but have
to carry out all operations with Simple Neurite Tracer manually. I seem
to vaguely remember having read somewhere that it is possible to use
Java commands from a Macro (I know I should probably learn to use Java,
but ...), but looking around I couldn't find any real relevant
information anywhere. Is this correct and if that is possible, can you
point me to any relevant information? Could that be a way around to
access functions in a plugin from a macro that are not macro recordable?

Thanks,
Volko


On 16/06/2016 19:28, Curtis Rueden wrote:

> Hi Volko,
>
> My lab does not use this plugin, so I do not know the answers to your
> questions. I'm sorry to say that the Simple Neurite Tracer is largely
> unmaintained now, since the original author left the ImageJ community. The
> core Fiji team is able to review and accept suggested code changes proposed
> by others, but we unfortunately do not have time to fix bugs ourselves.
>
> If any developers in the community are familiar with the Simple Neurite
> Tracer and want to adopt it, please post on the ImageJ Forum—that would be
> most welcome indeed.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - http://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Thu, May 26, 2016 at 1:11 AM, Volko Straub <[hidden email]> wrote:
>
>> Dear All,
>>
>> I have used Simple Neurite Tracer to trace neuronal morphologies. During
>> the analysis of the traces, I realised that some of the lower order side
>> branches are not correctly connected to their parent branch (must have
>> forgotten to press the branch modifier keys during the tracing). Is there a
>> simple/convenient way to connect two existing branches within Simple
>> Neurite Tracer (I don't seem to be able to find that option), or perhaps an
>> option to edit the trace files created by Simple Neurite Tracer.
>> On a related note, I was wondering whether there is a simple way to access
>> the path parameters such as start and end coordinates and path length from
>> a macro. I know that I can export them as a csv file, but it seems a bit
>> clunky to first export them as a csv file and then read the parameters from
>> there.
>> Any ideas/suggestions would be very much appreciated.
>>
>> Thanks,
>> Volko
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Re: Simple Neurite Tracer - Connecting existing branches

ctrueden
Hi Volko,

> I seem to vaguely remember having read somewhere that it is possible
> to use Java commands from a Macro (I know I should probably learn to
> use Java, but ...), but looking around I couldn't find any real
> relevant information anywhere. Is this correct and if that is
> possible, can you point me to any relevant information? Could that be
> a way around to access functions in a plugin from a macro that are not
> macro recordable?

Probably you mean the call macro function [1], which can call public static
Java methods which accept only string arguments. It can sometimes work
around non-macro-recordability, but it really depends on the Java API of
the plugin(s) in question. And often entails writing Java wrapper functions
of that nature.

Regards,
Curtis

[1] http://imagej.net/developer/macro/functions.html#call

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Thu, Jun 16, 2016 at 11:43 PM, Volko Straub <[hidden email]> wrote:

> Hi Curtis,
>
> Thanks for the response. It is a bit of a shame that Simple Neurite Tracer
> is not more actively maintained as I think that it does a great job.
> Unfortunately, a lack of expertise, programming skills and time prevents me
> from having a look at the actual code of the plugin (my 'programming' in
> ImageJ is restricted to writing Macros).
> This is also the biggest hurdle for me at the moment as the commands
> within the Simple Neurite Tracer plugin are not macro recordable, which
> means that I can open the Simple Neurite Tracer from a macro, but have to
> carry out all operations with Simple Neurite Tracer manually. I seem to
> vaguely remember having read somewhere that it is possible to use Java
> commands from a Macro (I know I should probably learn to use Java, but
> ...), but looking around I couldn't find any real relevant information
> anywhere. Is this correct and if that is possible, can you point me to any
> relevant information? Could that be a way around to access functions in a
> plugin from a macro that are not macro recordable?
>
> Thanks,
> Volko
>
>
>
> On 16/06/2016 19:28, Curtis Rueden wrote:
>
>> Hi Volko,
>>
>> My lab does not use this plugin, so I do not know the answers to your
>> questions. I'm sorry to say that the Simple Neurite Tracer is largely
>> unmaintained now, since the original author left the ImageJ community. The
>> core Fiji team is able to review and accept suggested code changes
>> proposed
>> by others, but we unfortunately do not have time to fix bugs ourselves.
>>
>> If any developers in the community are familiar with the Simple Neurite
>> Tracer and want to adopt it, please post on the ImageJ Forum—that would be
>> most welcome indeed.
>>
>> Regards,
>> Curtis
>>
>> --
>> Curtis Rueden
>> LOCI software architect - http://loci.wisc.edu/software
>> ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
>> Did you know ImageJ has a forum? http://forum.imagej.net/
>>
>>
>> On Thu, May 26, 2016 at 1:11 AM, Volko Straub <[hidden email]>
>> wrote:
>>
>> Dear All,
>>>
>>> I have used Simple Neurite Tracer to trace neuronal morphologies. During
>>> the analysis of the traces, I realised that some of the lower order side
>>> branches are not correctly connected to their parent branch (must have
>>> forgotten to press the branch modifier keys during the tracing). Is
>>> there a
>>> simple/convenient way to connect two existing branches within Simple
>>> Neurite Tracer (I don't seem to be able to find that option), or perhaps
>>> an
>>> option to edit the trace files created by Simple Neurite Tracer.
>>> On a related note, I was wondering whether there is a simple way to
>>> access
>>> the path parameters such as start and end coordinates and path length
>>> from
>>> a macro. I know that I can export them as a csv file, but it seems a bit
>>> clunky to first export them as a csv file and then read the parameters
>>> from
>>> there.
>>> Any ideas/suggestions would be very much appreciated.
>>>
>>> Thanks,
>>> Volko
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Simple Neurite Tracer - Connecting existing branches

Mimi
This post has NOT been accepted by the mailing list yet.
In reply to this post by Volko Straub
Hi there,

I'm having the exact same problem as you are. Did you manage to find a solution? I also missed a branch in one of the dendrites, and continued to complete the tracing for about 50 paths. Do you have any way to undo this also?

This is probably the biggest limitation in ImageJ and for those who are less tech-savy, it appears quite problematic!!

Thanks,
Mariam
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