2015Abrishami Movies - Revision history

Vahid abrishami: /* Related methods */

2015-06-22T10:53:54Z

Related methods

← Older revision		Revision as of 10:53, 22 June 2015
Line 29:		Line 29:

	== Related methods ==		== Related methods ==

			== Comments ==

Vahid abrishami: /* Related software */

2015-06-22T10:53:23Z

Related software

← Older revision		Revision as of 10:53, 22 June 2015
Line 27:		Line 27:

	http://scipion.cnb.csic.es/docs/bin/view/TWiki/WebHome		http://scipion.cnb.csic.es/docs/bin/view/TWiki/WebHome

			== Related methods ==

Vahid abrishami: /* Related methods */

2015-06-22T10:53:15Z

Related methods

← Older revision		Revision as of 10:53, 22 June 2015
Line 27:		Line 27:

	http://scipion.cnb.csic.es/docs/bin/view/TWiki/WebHome		http://scipion.cnb.csic.es/docs/bin/view/TWiki/WebHome


	~~== Related methods ==~~

Vahid abrishami: /* Related software */

2015-06-22T10:53:01Z

Related software

← Older revision		Revision as of 10:53, 22 June 2015
Line 27:		Line 27:

	http://scipion.cnb.csic.es/docs/bin/view/TWiki/WebHome		http://scipion.cnb.csic.es/docs/bin/view/TWiki/WebHome


			== Related methods ==

Vahid abrishami: /* Links */

2015-06-22T10:52:34Z

Links

← Older revision		Revision as of 10:52, 22 June 2015
Line 23:		Line 23:

	http://www.ncbi.nlm.nih.gov/pubmed/25681631		http://www.ncbi.nlm.nih.gov/pubmed/25681631

			== Related software ==

			http://scipion.cnb.csic.es/docs/bin/view/TWiki/WebHome

Vahid abrishami: /* Keywords */

2015-06-22T10:51:46Z

Keywords

← Older revision		Revision as of 10:51, 22 June 2015
Line 19:		Line 19:

	Direct detection devices, Beam induced motion, Single particle analysis, Electron microscopy		Direct detection devices, Beam induced motion, Single particle analysis, Electron microscopy

			== Links ==

			http://www.ncbi.nlm.nih.gov/pubmed/25681631

Vahid abrishami: /* Abstract */

2015-06-22T10:50:19Z

Abstract

← Older revision		Revision as of 10:50, 22 June 2015
Line 15:		Line 15:
	Optical Flow allows for quantitative analysis of the BIM pattern. The software that incorporates the		Optical Flow allows for quantitative analysis of the BIM pattern. The software that incorporates the
	new approach is available in XMIPP (http://xmipp.cnb.csic.es).		new approach is available in XMIPP (http://xmipp.cnb.csic.es).

			== Keywords ==

			Direct detection devices, Beam induced motion, Single particle analysis, Electron microscopy

Vahid abrishami: /* Keywords */

2015-06-22T10:50:06Z

Keywords

← Older revision		Revision as of 10:50, 22 June 2015
Line 2:		Line 2:

	Abrishami, V., Vargas, J., Li, X., Cheng, Y., Marabini, R., Sorzano, C. O. S., , J. M., Carazo. "Alignment of direct detection device micrographs using a robust Optical Flow approach." Journal of structural biology 189.3 (2015): 163-176.		Abrishami, V., Vargas, J., Li, X., Cheng, Y., Marabini, R., Sorzano, C. O. S., , J. M., Carazo. "Alignment of direct detection device micrographs using a robust Optical Flow approach." Journal of structural biology 189.3 (2015): 163-176.

	~~== Keywords ==~~

	~~Direct detection devices, Beam induced motion, Single particle analysis, Electron microscopy~~

	== Abstract ==		== Abstract ==

Vahid abrishami: /* Citation */

2015-06-22T10:49:55Z

Citation

← Older revision		Revision as of 10:49, 22 June 2015
Line 2:		Line 2:

	Abrishami, V., Vargas, J., Li, X., Cheng, Y., Marabini, R., Sorzano, C. O. S., , J. M., Carazo. "Alignment of direct detection device micrographs using a robust Optical Flow approach." Journal of structural biology 189.3 (2015): 163-176.		Abrishami, V., Vargas, J., Li, X., Cheng, Y., Marabini, R., Sorzano, C. O. S., , J. M., Carazo. "Alignment of direct detection device micrographs using a robust Optical Flow approach." Journal of structural biology 189.3 (2015): 163-176.

			== Keywords ==

			Direct detection devices, Beam induced motion, Single particle analysis, Electron microscopy

	== Abstract ==		== Abstract ==

Vahid abrishami: /* Citation */

2015-06-22T10:48:25Z

Citation

← Older revision		Revision as of 10:48, 22 June 2015
Line 2:		Line 2:

	Abrishami, V., Vargas, J., Li, X., Cheng, Y., Marabini, R., Sorzano, C. O. S., , J. M., Carazo. "Alignment of direct detection device micrographs using a robust Optical Flow approach." Journal of structural biology 189.3 (2015): 163-176.		Abrishami, V., Vargas, J., Li, X., Cheng, Y., Marabini, R., Sorzano, C. O. S., , J. M., Carazo. "Alignment of direct detection device micrographs using a robust Optical Flow approach." Journal of structural biology 189.3 (2015): 163-176.

			== Abstract ==

			The introduction of direct detection devices in cryo-EM has shown that specimens present beam-induced
			motion (BIM). Consequently, in this work, we develop a BIM correction method at the image level, resulting
			in an integrated image in which the in-plane BIM blurring is compensated prior to particle picking.
			The methodology is based on a robust Optical Flow (OF) approach that can efficiently correct for local
			movements in a rapid manner. The OF works particularly well if the BIM pattern presents a substantial
			degree of local movements, which occurs in our data sets for Falcon II data. However, for those cases in
			which the BIM pattern corresponds to global movements, we have found it advantageous to first run a
			global motion correction approach and to subsequently apply OF. Additionally, spatial analysis of the
			Optical Flow allows for quantitative analysis of the BIM pattern. The software that incorporates the
			new approach is available in XMIPP (http://xmipp.cnb.csic.es).