Trouble quantifying neurite outgrowth from explant

[Marcus_pocus]

Dear all,

I'm very new to the imageJ software and am having quite a bit of trouble finding a time efficient way to measure three parameters in the following type of image.



The parameters I'm looking to measure are:
- Surface covered by the neurites
- Neurite density
- Average neurite lenght

Any help of advice would be greatly appreciated!

Cheers,

MP

[carlo bianco]

In my opinion you can try
an efficient thresholding (invert+manual tresholding)
followed by manual selection of roi. there  is also the ad hoc plugin
http://www.imagescience.org/meijering/software/neuronj/
but I never used it, and seems to be more useful.
With an other approach you can use grids and assess the presence/absence
of dendritic branch (is a systematic sampling )
If you extract the boundary and skeletonize it, you can evaluate the compelxity of branching
by means on fractal box counting, the fractal dimension
can be viewed as a space filling capacity syntetic indicator
and is used in quantitative neuropathology.
best wishes for your research
carlo bianco
Bologna University



Il Venerdì 8 Novembre 2013 12:39, Marcus_pocus <[hidden email]> ha scritto:
 
Dear all,

I'm very new to the imageJ software and am having quite a bit of trouble
finding a time efficient way to measure three parameters in the following
type of image.

<http://imagej.1557.x6.nabble.com/file/n5005499/Expl_2_ipsi_-_photo_for_imageJ_forum.jpg>

The parameters I'm looking to measure are:
- Surface covered by the neurites
- Neurite density
- Average neurite lenght

Any help of advice would be greatly appreciated!

Cheers,

MP






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[Marcus_pocus]

Thanks for your answer!

The problem is that the images aren't clear enough to totally exclude the background and specks and include all the neurites, so use of NeuronJ or the skeletonize function aren't possible (unless I'm mistaken). I'm currently doing immunofluorescence stainings in order the obtain better images.

As for these brightfield pictures, I was initially thinking of something along the line of this:

Selecting 2 ROIS corresponding to the explant and the halo of neurites and measuring the overall area that is covered by the neurites, the optical density of the "neurite zone" and the average distance between the two ROIs. All these being quite indirect measures of neurite outgrowth but still better than nothing.

I imagine that measuring the area and the OD must be quite straightforward however I don't have a clue as to how I could measure the "average neurite lenght". Any tips?

Thanks once more to any benevolent helpers!

Cheers,

Marc

[Marcus_pocus]

2013/11/8 Marcus_pocus [via ImageJ] <[hidden email]>

Thanks for your answer!

The problem is that the images aren't clear enough to totally exclude the background and specks and include all the neurites, so use of NeuronJ or the skeletonize function aren't possible (unless I'm mistaken). I'm currently doing immunofluorescence stainings in order the obtain better images.

As for these brightfield pictures, I was initially thinking of something along the line of this:

Selecting 2 ROIS corresponding to the explant and the halo of neurites and measuring the overall area that is covered by the neurites, the optical density of the "neurite zone" and the average distance between the two ROIs. All these being quite indirect measures of neurite outgrowth but still better than nothing.

I imagine that measuring the area and the OD must be quite straightforward however I don't have a clue as to how I could measure the "average neurite lenght". Any tips?

Thanks once more to any benevolent helpers!

Cheers,

Marc

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[chris elliott]

How about a Scholl analysis ? - counting the ring/neurite crossings ?
chris
On 8 Nov 2013, at 14:08, Marcus_pocus <[hidden email]> wrote:

> Thanks for your answer!
>
> The problem is that the images aren't clear enough to totally exclude the
> background and specks and include all the neurites, so use of NeuronJ or the
> skeletonize function aren't possible (unless I'm mistaken). I'm currently
> doing immunofluorescence stainings in order the obtain better images.
>
> As for these brightfield pictures, I was initially thinking of something
> along the line of this:
> <http://imagej.1557.x6.nabble.com/file/n5005503/Expl_2_ipsi_-_photo_for_imageJ_forum_2.jpg>
> Selecting 2 ROIS corresponding to the explant and the halo of neurites and
> measuring the *overall area *that is covered by the neurites, the *optical
> density* of the "neurite zone" and the *average distance* between the two
> ROIs. All these being quite indirect measures of neurite outgrowth but still
> better than nothing.
>
> I imagine that measuring the *area *and the *OD *must be quite
> straightforward however I don't have a clue as to how I could measure the
> "average neurite lenght". Any tips?
>
> Thanks once more to any benevolent helpers!
>
> Cheers,
>
> Marc
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Trouble-quantifying-neurite-outgrowth-from-explant-tp5005499p5005503.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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