How do I control NeuronJ from a Macro?

[Jeanine Hinterneder]

Hello All-

 I have traced a bunch of images of neurons in NeuronJ and would like
 to now go through each image in the folder and take snapshots of the
 tracings and save them to a separate folder.  I have created a macro
 so far to do on each individual image (See below).
 However, it takes me a long time (and lots of individual clicks of the
 mouse) to separately open each image with NeuronJ and take Snapshots
 of each image.  I would LOVE to be able to batch process this folder!
 (Or, at the least to run the macro in a loop through a folder of
 images and have it run the open function and pause for me to select
 the next image in the folder each time.)

 Does anyone know why I can't use the Macro Recorder the "Snapshot"
 function or "Open" functions from the NeuronJ toolbar?
 Can anyone tell me if there's a way to run these commands from a Macro?

 Thanks a bunch!

 Jeanine

[lechristophe]

NeuronJ has a built-in function that opens the next image in a folder
by pressing the right arrow key, and the previous on with the left
arrow. If you select the "autosave" option, you can very quickly
browse from one image to another, and even trave neurites on each one
and save them on the fly, as explained here :
http://www.imagescience.org/meijering/software/neuronj/manual.html

As an aside, NeuronJ has a lot of these small tips, like pressing
shift to override the automatic detection of neurite on a segment and
use a straight line instead, or override the auto placement to
precisely define a point under your cursor.

In fact NeuronJ is so efficient to rapidly trace neurites on 2D images
(compared to Simple neurite tracer, whcih is more powerful but has a
very steep learning curve), but is also so detached from the rest of
ImageJ that I'm now writing a macro that translate NeuronJ trace files
into ROI manager line ROIs, allowing to access the extended
measurement capabilities of ImageJ with NeuronJ-based traces.

Christophe

On Mon, Aug 30, 2010 at 22:58, Jeanine Hinterneder <[hidden email]> wrote:

> Hello All-
>
> I have traced a bunch of images of neurons in NeuronJ and would like
> to now go through each image in the folder and take snapshots of the
> tracings and save them to a separate folder.  I have created a macro
> so far to do on each individual image (See below).
> However, it takes me a long time (and lots of individual clicks of the
> mouse) to separately open each image with NeuronJ and take Snapshots
> of each image.  I would LOVE to be able to batch process this folder!
> (Or, at the least to run the macro in a loop through a folder of
> images and have it run the open function and pause for me to select
> the next image in the folder each time.)
>
> Does anyone know why I can't use the Macro Recorder the "Snapshot"
> function or "Open" functions from the NeuronJ toolbar?
> Can anyone tell me if there's a way to run these commands from a Macro?
>
> Thanks a bunch!
>
> Jeanine
>

[Dan McDonald]

Christophe,

Excellent. This will be a wonderful enhancement. I look forward to it.
Thank you.

DAn

Daniel W. McDonald, President
Phenotype Screening Corporation
4028 Papermill Rd, Suite 10
Knoxville, TN 37909
[phone]
 
Our product, RootViz FS, was a 2007 R&D100 Award Winner. Rated as one of the
100 most technologically significant products introduced into the
marketplace in the prior year.
-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Christophe Leterrier
Sent: Monday, August 30, 2010 5:31 PM
To: [hidden email]
Subject: Re: How do I control NeuronJ from a Macro?

NeuronJ has a built-in function that opens the next image in a folder
by pressing the right arrow key, and the previous on with the left
arrow. If you select the "autosave" option, you can very quickly
browse from one image to another, and even trave neurites on each one
and save them on the fly, as explained here :
http://www.imagescience.org/meijering/software/neuronj/manual.html

As an aside, NeuronJ has a lot of these small tips, like pressing
shift to override the automatic detection of neurite on a segment and
use a straight line instead, or override the auto placement to
precisely define a point under your cursor.

In fact NeuronJ is so efficient to rapidly trace neurites on 2D images
(compared to Simple neurite tracer, whcih is more powerful but has a
very steep learning curve), but is also so detached from the rest of
ImageJ that I'm now writing a macro that translate NeuronJ trace files
into ROI manager line ROIs, allowing to access the extended
measurement capabilities of ImageJ with NeuronJ-based traces.

Christophe

On Mon, Aug 30, 2010 at 22:58, Jeanine Hinterneder <[hidden email]>
wrote:

> Hello All-
>
> I have traced a bunch of images of neurons in NeuronJ and would like
> to now go through each image in the folder and take snapshots of the
> tracings and save them to a separate folder.  I have created a macro
> so far to do on each individual image (See below).
> However, it takes me a long time (and lots of individual clicks of the
> mouse) to separately open each image with NeuronJ and take Snapshots
> of each image.  I would LOVE to be able to batch process this folder!
> (Or, at the least to run the macro in a loop through a folder of
> images and have it run the open function and pause for me to select
> the next image in the folder each time.)
>
> Does anyone know why I can't use the Macro Recorder the "Snapshot"
> function or "Open" functions from the NeuronJ toolbar?
> Can anyone tell me if there's a way to run these commands from a Macro?
>
> Thanks a bunch!
>
> Jeanine
>