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xulabs / aitom

AI for tomography
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Make particle picking working #3

Open xulabs opened 5 years ago

xulabs commented 5 years ago

related functions are inside aitom.aitom.pick.dog.particle_picking_dog__util

can start with making it working on a simulated tomogram

Then make it working on a publically avaliable real tomogram, such as https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10045/

Related paper: Pei L, Xu M, Frazier Z, Alber F. Simulating Cryo-Electron Tomograms of Crowded Mixtures of Macromolecular Complexes and Assessment of Particle Picking. BMC Bioinformatics. 2016; 17: 405.

xulabs commented 5 years ago

Can start with this tomogram: http://ftp.ebi.ac.uk/pub/databases/empiar/archive/10045/data/ribosomes/Tomograms/05/IS002_291013_005.mrc

first reduce its size through bining, see here:

https://github.com/xulabs/aitom/wiki/Tomogram-manipulation

xulabs commented 5 years ago

TODO: replace with a larger tomogram upload imod display code

xulabs commented 5 years ago

display code added to aitom/pick/plot/particle_location_display_imod.py

xulabs commented 5 years ago

@wobushiyitouzhu

Can start with this tomogram: http://ftp.ebi.ac.uk/pub/databases/empiar/archive/10045/data/ribosomes/Tomograms/05/IS002_291013_005.mrc

first reduce its size through bining, see here:

https://github.com/xulabs/aitom/wiki/Tomogram-manipulation

xulabs commented 5 years ago

@wobushiyitouzhu please also explain the input parameters and output data format by adding comments to corresponding functions.