Purifying images for connectivity

[Sara M]

Dear Michael,

I have been using the purify tool in Bone J prior to calculating the
connectivity for trabcular Bone.

I have found that the purification process takes quite long (approx 30
mins) for some of my images ( around 850MB in size).

As such I was wondering if there was anyway of speeding this process
up and whether this would affect the resulting connectivity values
that are generated from the purified image?

Kind Regards,
Sara

[Michael Doube]

Dear Sara,

> I have found that the purification process takes quite long (approx 30
> mins) for some of my images ( around 850MB in size).

That sounds about right (unfortunately).

> As such I was wondering if there was anyway of speeding this process
> up

1: use the multithreaded particle labelling algorithm on smaller chunks
(2) and on a machine with very many CPU cores.

2: try the linear particle labelling algorithm - you may need a machine
with a lot of RAM. Good news: RAM got really cheap in the last year.

3: if your images are in high resolution, you could consider
downsampling prior to binarization

> and whether this would affect the resulting connectivity values
> that are generated from the purified image?

1: and 2: - Shouldn't change Conn.D. It is a bug if that is what you find.

3: probably because small details will get changed

Michael