[chimerax-users] Automating Map segment

[Tom Goddard]

To group by connectivity looks like you need to add

	d._group_con.value = True

To figure out this stuff you would need to look at the Segger user interface code, it is in the ChimeraX distribution (under site-packages/chimerax/segger/segment_dialog.py) or on GitHub

	https://github.com/tomgoddard/segger/blob/master/Segger/src/segment_dialog.py <https://github.com/tomgoddard/segger/blob/master/Segger/src/segment_dialog.py>

  Tom


> On Jul 30, 2021, at 10:42 AM, Sam W Marchant <smarchant at UCSD.EDU> wrote:
> 
> Thanks so much im trying to group by connectivity and I am having trouble finding the right line of code to add that ability. Any thoughts?
> 
>> On Jul 29, 2021, at 3:56 PM, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
>> 
>> Hi Sam,
>> 
>>   I did an initial port of Segger from Chimera to ChimeraX (also called Segment Map) but that code was written by Greg Pintilie and he has not worked the ChimeraX version so there is no new command to run it in a script.  It would probably not be too hard to write some Python to run it.  The Chimera script mentioned in the mailing list is attached to my message about it. 
>> 
>> https://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-October/013979.html <https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_pipermail_chimera-2Dusers_2017-2DOctober_013979.html&d=DwMFAg&c=-35OiAkTchMrZOngvJPOeA&r=uD_TSVq4meN3oIoPbsDm3-oav9mCWFaQQOLM2ohEUNE&m=HhK7h-se-w1v6yFJwYxWsYLZcOp9Tci-UFJyeizhnM0&s=TD_p3CR-6e4xyrogHNJRNuDvlxcDsQPjRgrUt7efVgg&e=>
>> 
>> That won't work in ChimeraX, but here I attach the equivalent for ChimeraX.
>> 
>>   Segger was developed to segment molecules in EM maps, so I have doubts that it will do much good for your light microscopy.  But you can decide that by running it by hand on some time steps and see if you like the result.
>> 
>>   Here is a different approach we used to quantify protrusions of crawling neutrophils in light sheet microscopy by placing markers that might be of interest.
>> 
>> https://www.cgl.ucsf.edu/chimera/data/protrusion-sep2015/protrusions.html <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cgl.ucsf.edu_chimera_data_protrusion-2Dsep2015_protrusions.html&d=DwMFAg&c=-35OiAkTchMrZOngvJPOeA&r=uD_TSVq4meN3oIoPbsDm3-oav9mCWFaQQOLM2ohEUNE&m=HhK7h-se-w1v6yFJwYxWsYLZcOp9Tci-UFJyeizhnM0&s=VLRfZxfLgNIrgf0QyH12Ge2-HusBDRyk9ii1wtS4ny8&e=>
>> 
>>   Tom
>> 
>> 
>> 
>>> On Jul 29, 2021, at 3:24 PM, Sam W Marchant via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>>> 
>>> Hi,
>>> I am looking to apply the Map Segmenting to multiple time series of light sheet imaging and so I was wondering if there is either a command or a python function to automate the process. It looks here <https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_pipermail_chimera-2Dusers_2017-2DOctober_013980.html&d=DwMCAg&c=-35OiAkTchMrZOngvJPOeA&r=uD_TSVq4meN3oIoPbsDm3-oav9mCWFaQQOLM2ohEUNE&m=HhK7h-se-w1v6yFJwYxWsYLZcOp9Tci-UFJyeizhnM0&s=Unt7TSRk5c2Ad_Ra88KwRwXRUQHvZiDihlSmvQL7BJQ&e=> that you said it was going to be added to ChimeraX but I cannot find any info on how to do it. If not you mentioned a script in this answer, could you potentially send that to me?
>>> Thanks,
>>> Sam Marchant.
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>> 
>> <segscript.py>
> 

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