[Chimera-users] Segger : command line

agnel-praveen.joseph at stfc.ac.uk agnel-praveen.joseph at stfc.ac.uk
Fri Jan 24 02:51:18 PST 2014

Many thanks. I will have a look at the scripts and extract the required functions and classes. This is very helpful.

From: Tom Goddard [mailto:goddard at sonic.net]
Sent: 24 January 2014 02:51
To: Joseph, Agnel Praveen (STFC,RAL,SC)
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Segger : command line

There is no Chimera command to run Segger so you would need to use Python code to automate it on a set of volumes.  The Segger Python code is very messy so this will be difficult.  If you are an experienced Python programmer then your aim would be to write a Python script that runs within Chimera opens the first map, creates a Segmentation instance from the class defined in


calls the smooth_and_group(steps, sdev) method, and writes out the resulting segmentation with the write_segmentation() routine in


or the writing could be done with the Chimera "segment" command to export a mask file


The Segger code is complicated with lots of code that was testing experimental features, so if you are not an experienced Python programmer I'm afraid it will not be possible to automate processing using it.

It would be nice if the Chimera segment command let you run the Segger algorithm -- then your processing of many maps would be much easier.  We will keep that in mind for the next generation of Chimera which we are currently working on.


On Jan 23, 2014, at 5:04 AM, wrote:


I would like to automate watershed segmentation (Segger) on a set of volumes. Given that I have the details on the volume threshold, number of smoothing steps and minimum voxels in each region, is there a way to automate segmentation with different parameter inputs?

Many Thanks.

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