CoSS: /* Abstract */

2015-05-11T12:32:12Z

Abstract

← Older revision		Revision as of 12:32, 11 May 2015
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	by electron microscopy by single		by electron microscopy by single
	particle techniques. The impressive achievements in		particle techniques. The impressive achievements in
	single particle ~~reconstr~~		single particle reconstruction fuel its expansion
	~~uction~~ fuel its expansion		beyond a small community of image processing experts. This poses the risk of inappropriate data
	beyond a small community of image pr		processing with dubious results. Nowhere is it more clearly
	~~ocessing~~ experts. This poses th		illustrated than in
	e risk of inappropriate data		the recovery of a
	processing with dubious results. ~~Nowh~~		reference density map from pure noise aligned to that map—a phantom
	~~ere~~ is it more clearly		in the noise. Appropriate use
	illustrated than in		of existing validating methods such as resolution-limited alignment and the processing of
	the recovery of a
	reference density map from pure ~~noi~~
	se aligned to that map—a phantom
	in the noise. Appropriate use
	of existing validating methods such as ~~resolu~~
	~~tion~~-limited alignment and the processing of
	independent data sets (“gold standard”) avoid		independent data sets (“gold standard”) avoid
	this pitfall. However, these methods can be		this pitfall. However, these methods can be
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	the micrographs? In stead of viewing the phantom		the micrographs? In stead of viewing the phantom
	emerging from noise as a cautionary		emerging from noise as a cautionary
	tale, it should be used as a ~~defi~~		tale, it should be used as a defining baseline. Any map is always
	~~ning~~ baseline. Any map is always		recoverable from noise images, provided a sufficient number of images are aligned and used in
	recoverable from noise images, provided a ~~sufficie~~		reconstruction. However, with smaller numbers of images, the expected
	nt number of images are aligned and used in
	reconstruction. However, with ~~smalle~~
	r numbers of images, the expected
	coherence in the		coherence in the
	real particle		real particle
	images should yield better ~~reconstr~~		images should yield better reconstructions than equivalent number
	~~uctions~~ than equivalent number
	s of noise or background images,		s of noise or background images,
	even without masking or imposing resolution limits		even without masking or imposing resolution limits
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	is therefore a simple alignment of a limited number		is therefore a simple alignment of a limited number
	of micrograph and noise images against the final		of micrograph and noise images against the final
	reconstruction as reference, ~~demons~~		reconstruction as reference, demonstrating that the micrograph images
	~~trating~~ that the micrograph images		yield a better reconstruction. I
	yield a better reconstruction. I
	examine synthetic cases to relate the resolution of a reconstruction to the alignment error as a		examine synthetic cases to relate the resolution of a reconstruction to the alignment error as a
	function of the signal-to-~~noi~~		function of the signal-to-noise ratio. I also administered the test to real cases of publicly available
	se ratio. I also ~~administer~~		data. Adopting such a test can aid the microscopist in assessing
	ed the test to real cases of publicly available		the usefulness of the micrographs taken before committing to lengthy processing with questionable outcomes.
	data. Adopting such a test can ai
	d the microscopist in assessing
	the usefulness of the micrographs
	taken before committing to lengthy processing with questionable outcomes.

	== Keywords ==		== Keywords ==

CoSS: Created page with "== Citation == Heymann, B. Validation of 3DEM Reconstructions: The phantom in the noise AIMS Biophysics, 2015, 2, 21-35 == Abstract == Validation is a necessity to trust t..."

2015-05-11T12:31:23Z

Created page with "== Citation == Heymann, B. Validation of 3DEM Reconstructions: The phantom in the noise AIMS Biophysics, 2015, 2, 21-35 == Abstract == Validation is a necessity to trust t..."

New page

== Citation ==

Heymann, B. Validation of 3DEM Reconstructions: The phantom in the noise AIMS Biophysics, 2015, 2, 21-35

== Abstract ==

Validation is a necessity to
trust the structures solved
by electron microscopy by single
particle techniques. The impressive achievements in
single particle reconstr
uction fuel its expansion
beyond a small community of image pr
ocessing experts. This poses th
e risk of inappropriate data
processing with dubious results. Nowh
ere is it more clearly
illustrated than in
the recovery of a
reference density map from pure noi
se aligned to that map—a phantom
in the noise. Appropriate use
of existing validating methods such as resolu
tion-limited alignment and the processing of
independent data sets (“gold standard”) avoid
this pitfall. However, these methods can be
undermined by biases introduced in
various subtle ways. How can we
test that a map is a coherent
structure present in the images selected from
the micrographs? In stead of viewing the phantom
emerging from noise as a cautionary
tale, it should be used as a defi
ning baseline. Any map is always
recoverable from noise images, provided a sufficie
nt number of images are aligned and used in
reconstruction. However, with smalle
r numbers of images, the expected
coherence in the
real particle
images should yield better reconstr
uctions than equivalent number
s of noise or background images,
even without masking or imposing resolution limits
as potential biases. The
validation test proposed
is therefore a simple alignment of a limited number
of micrograph and noise images against the final
reconstruction as reference, demons
trating that the micrograph images
yield a better reconstruction. I
examine synthetic cases to relate the resolution of a reconstruction to the alignment error as a
function of the signal-to-noi
se ratio. I also administer
ed the test to real cases of publicly available
data. Adopting such a test can ai
d the microscopist in assessing
the usefulness of the micrographs
taken before committing to lengthy processing with questionable outcomes.

== Keywords ==

Validation

== Links ==

http://www.aimspress.com/aimsbpoa/ch/reader/create_pdf.aspx?file_no=Biophys-10&year_id=2015&quarter_id=1&falg=1

== Related software ==

== Related methods ==

== Comments ==

2015Heymann Alignability - Revision history

CoSS: /* Abstract */

CoSS: Created page with "== Citation == Heymann, B. Validation of 3DEM Reconstructions: The phantom in the noise AIMS Biophysics, 2015, 2, 21-35 == Abstract == Validation is a necessity to trust t..."