Difference between revisions of "Tomography processing notes"

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m (On gold fiducials)
 
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Apparently in theory there's                                                                                         
 
Apparently in theory there's                                                                                         
* Au<sub>11</sub> (0.8mn) a.k.a. undecagold,
+
* Au<sub>11</sub> (0.8mn) a.k.a. undecagold
* Au<sub>25</sub> (0.9mn),
+
* Au<sub>25</sub> (0.9mn)
* Au<sub>38</sub> (1.1nm),
+
* Au<sub>38</sub> (1.1nm)
* Au<sub>68</sub> (1.3nm),
+
* Au<sub>68</sub> (1.3nm)
* 1.4nm, often referred to as nanogold,
+
* 1.4nm, often referred to as nanogold{{verify}}
* Au<sub>102</sub> (1.5nm),
+
* Au<sub>102</sub> (1.5nm)
* 1.8nm, a.k.a. Ni-NTA–Nanogold{{verify}}),
+
* 1.8nm (a.k.a. Ni-NTA–Nanogold{{verify}})
 
* Au<sub>114</sub> (2.0nm)
 
* Au<sub>114</sub> (2.0nm)
 
* Much larger is [https://en.wikipedia.org/wiki/Colloidal_gold colloidal gold] {{comment|(so these sizes are a little more approximate)}}, often one of
 
* Much larger is [https://en.wikipedia.org/wiki/Colloidal_gold colloidal gold] {{comment|(so these sizes are a little more approximate)}}, often one of
Line 20: Line 20:
 
** 20nm
 
** 20nm
 
** 25nm
 
** 25nm
 +
  
 
Apparently most commonly it's 5nm or 10nm, sometimes nanogold{{verify}}.
 
Apparently most commonly it's 5nm or 10nm, sometimes nanogold{{verify}}.
  
See also "[Site-specific biomolecule labeling with gold clusters." ([https://www.ncbi.nlm.nih.gov/pubmed/20887859 PMC3568671])
+
See also  
 
+
: "Site-specific biomolecule labeling with gold clusters." ([https://www.ncbi.nlm.nih.gov/pubmed/20887859 PMC3568671])
 
+
: https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/nanogold
 
+
 
+
  
 
====In general====
 
====In general====
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A typical approach is described in imod. See e.g.
+
A typical approach is described e.g. in imod. See e.g.
 
: the overall diagram in [https://www.sciencedirect.com/science/article/pii/S1047847716301526 "Automated tilt series alignment and tomographic reconstruction in IMOD"]
 
: the overall diagram in [https://www.sciencedirect.com/science/article/pii/S1047847716301526 "Automated tilt series alignment and tomographic reconstruction in IMOD"]
 
: See also [https://bio3d.colorado.edu/imod/doc/tomoguide.html#TOP "Tomography Guide for IMOD Version 4.9"]
 
: See also [https://bio3d.colorado.edu/imod/doc/tomoguide.html#TOP "Tomography Guide for IMOD Version 4.9"]
Line 42: Line 41:
  
 
Required input  
 
Required input  
* a series of images with roughly known angles (=a tilt series)
+
* a series of images - a tilt series
* said angles
+
* roughly known angles for each such image
 
: in IMOD: MRC header, text file, or given interval
 
: in IMOD: MRC header, text file, or given interval
* tilt axis angle
+
* tilt axis angle (=basically the rotation between sensor/image and tilt axis, so the direction it rotates on within the image. It would be nice if this were mechanically aligned to the sensor('s longest dimension), but rarely true for practical reasons)
: theoretically ideally perpendicular to sensor('s longest dimension), but rarely true for practical reasons
+
 
: if wrong, the coarse alignment will fail
 
: if wrong, the coarse alignment will fail
 
: &#xB1;5 degrees is fine because it's usually a parameter it's finding in fine alignment
 
: &#xB1;5 degrees is fine because it's usually a parameter it's finding in fine alignment
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Useful input:
 
Useful input:
* Bead size helps find beads.
+
* knowing fiducial bead size eases finding them
  
 
* Target bead amount helps using what you have.
 
* Target bead amount helps using what you have.
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: used to not make the back-projected volume much larger than the sample (roughly "you can stop this far away from the beads")
 
: used to not make the back-projected volume much larger than the sample (roughly "you can stop this far away from the beads")
 
: also relevant to rotating the sample within that volume to align with one axis, for more sensible slicing, and smaller volume
 
: also relevant to rotating the sample within that volume to align with one axis, for more sensible slicing, and smaller volume
-->
 
  
* optional: dark/blank images
 
  
* remove X-rays, pixel defects
+
: '''Steps''', roughly
 +
 
 +
 
 +
optional: '''remove dark/blank images'''
 +
 
 +
'''remove X-rays''', pixel defects
 
: useful for normalization step
 
: useful for normalization step
 
: IMOD: ccderaser <!--(defaults usually okay)-->
 
: IMOD: ccderaser <!--(defaults usually okay)-->
  
* Rough alignment
+
 
 +
'''Rough alignment'''
 
: basically, minimize it jumping about
 
: basically, minimize it jumping about
 
: otherwise not solving anything, but it assists fine alinment
 
: otherwise not solving anything, but it assists fine alinment
 
: (e.g. somewhat specialized cross-correlation)
 
: (e.g. somewhat specialized cross-correlation)
: IMOD: tiltxcorr, creates .preali
+
: IMOD: tiltxcorr <!--, creates .preali-->
  
* Finer alignment, by one of:
 
** fiducial alignment (fiducials are small high-contrast things, typically gold beads)
 
** fiducialless alignment, e.g. patch tracking
 
** skipping (effectively assumes rough alignment is enough, which it basically never is)
 
  
* combine aligned images into stack
+
'''Finer alignment''', by one of:
 +
* alignment using fiducial model (fiducials are small high-contrast things, typically gold beads)<!--
 +
: IMOD: autofidseed (a wrapper around imodfindbeads); beadtrack (track initial set over the angles); tiltalign (solves alignment given fiducial tracking)  -->
 +
* fiducialless alignment, e.g. patch tracking / feature tracking
 +
* skipping (effectively assumes rough alignment is enough, which it basically never is)
  
* correct CTF (optional)
+
 
 +
'''model/correct CTF''' (optional)
 
: only really required for higher resolution, which you may not need
 
: only really required for higher resolution, which you may not need
  
* remove fiducial markers from images
+
 
 +
'''remove fiducial markers''' from images
 
: would be disturbing influence in tomogram
 
: would be disturbing influence in tomogram
  
* filtering
 
  
* make tomogram from the stack
+
'''filtering'''
** IMOD: weighted backprojection (WBP), or SIRT (Simultaneous Iterative Reconstruction Technique)
+
  
* cut out things that aren't specimen (optional, but rather practical)
 
  
* noise reduction via NAD (nonlinear anisotropic diffusion) filter (optional)
+
'''make tomogram''' from the stack
 +
* e.g. (Weighted) BackProjection (WBP), or SIRT (Simultaneous Iterative Reconstruction Technique)
 +
<!--
 +
: IMOD: tilt
 +
:: if parallelized, splittilt; tilt; (fixboundaries, collectmmm, b3dremove)
 +
 
 +
 
 +
: , cryoposition,
 +
-->
 +
 
 +
 
 +
'''slice out just the specimen''' (optional, but rather practical)
 +
 
 +
Optional: '''noise reduction''' via NAD (nonlinear anisotropic diffusion) filter
 +
 
 +
 
 +
Where applicable: '''combine dual axis''' tomogram
 +
 
 +
 
 +
Where useful: Subvolume averaging
 +
: if you have multiple of the same thing within a tomogram that you want to combine (sort of single particle style)
 +
 
  
* where applicable: combine dual axis tomogram
 
  
* Optional: Subvolume averaging (if you have multiple of the same thing within a tomogram that you want to combine (sort of single particle style)
 
  
  
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: but also requires and kicking out the ones that seem to disagree with the consensus,
 
: but also requires and kicking out the ones that seem to disagree with the consensus,
 
: because a few bad cases would throw off otherwise detailed averages.
 
: because a few bad cases would throw off otherwise detailed averages.
<!--: apparenting erring on the high side with fiducial size (and sometimes amount?) seems to be useful-->
+
<!--: apparently erring on the high side with fiducial size seems to be useful-->
 +
: IMOD: imodfindbeads, autofidseed, others
 +
 
 +
* IMOD goes to 3D twice, first for something to work on, later for a cleaned version. There seem to be a few reasons for this. <!--
 +
: it may be easier to find/verify beads in 3D, but it's easier to remove beads in 2D, so you basically go through things twice.
 +
:
 +
-->
  
 
===(semi)automated===
 
===(semi)automated===
 
Etomo runs you through the steps with some interaction in each.
 
Etomo runs you through the steps with some interaction in each.
  
 +
<!--
 +
to run com files, see subm
 +
-->
  
 
'''batchruntomo''' is essentially a job manager  
 
'''batchruntomo''' is essentially a job manager  
Line 123: Line 152:
 
Directives are sorted into:
 
Directives are sorted into:
 
* setupset - mostly describes collection and dataset
 
* setupset - mostly describes collection and dataset
* com-param - parameters for programs (like in .com files)
+
* com-param - parameters for programs (like those in .com files)
 
* run-time - parameters interpreted by batchruntomo or etomo {{verify}}
 
* run-time - parameters interpreted by batchruntomo or etomo {{verify}}
 
 
 
 
 
 
  
 
===Unsorted===
 
===Unsorted===

Latest revision as of 00:00, 31 August 2021

This article/section is a stub — probably a pile of half-sorted notes, is not well-checked so may have incorrect bits. (Feel free to ignore, fix, or tell me)

See also EM software notes

On gold fiducials

Apparently in theory there's

  • Au11 (0.8mn) a.k.a. undecagold
  • Au25 (0.9mn)
  • Au38 (1.1nm)
  • Au68 (1.3nm)
  • 1.4nm, often referred to as nanogold(verify)
  • Au102 (1.5nm)
  • 1.8nm (a.k.a. Ni-NTA–Nanogold(verify))
  • Au114 (2.0nm)
  • Much larger is colloidal gold (so these sizes are a little more approximate), often one of
    • 5nm
    • 10nm
    • 15nm
    • 20nm
    • 25nm


Apparently most commonly it's 5nm or 10nm, sometimes nanogold(verify).

See also

"Site-specific biomolecule labeling with gold clusters." (PMC3568671)
https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/nanogold

In general

The overall steps in reconstruction


A typical approach is described e.g. in imod. See e.g.

the overall diagram in "Automated tilt series alignment and tomographic reconstruction in IMOD"
See also "Tomography Guide for IMOD Version 4.9"
and a list of parts (some optional) in the batchruntomo man page.
and its tutorial https://bio3d.colorado.edu/imod/doc/batchExample.html


Required input

  • a series of images - a tilt series
  • roughly known angles for each such image
in IMOD: MRC header, text file, or given interval
  • tilt axis angle (=basically the rotation between sensor/image and tilt axis, so the direction it rotates on within the image. It would be nice if this were mechanically aligned to the sensor('s longest dimension), but rarely true for practical reasons)
if wrong, the coarse alignment will fail
±5 degrees is fine because it's usually a parameter it's finding in fine alignment
...but coarse alignment will probably fail if it's more than ~5 degrees off (because it's trying to accounting for the direction things squeeze in(verify))
IMOD: MRC header, or given value


Useful input:

  • knowing fiducial bead size eases finding them
  • Target bead amount helps using what you have.
  • Sample thickness
can be calculated from bead set (but not under all conditions, so a sensible fallback value can helps)
used to not make the back-projected volume much larger than the sample (roughly "you can stop this far away from the beads")
also relevant to rotating the sample within that volume to align with one axis, for more sensible slicing, and smaller volume


Steps, roughly


optional: remove dark/blank images

remove X-rays, pixel defects

useful for normalization step
IMOD: ccderaser


Rough alignment

basically, minimize it jumping about
otherwise not solving anything, but it assists fine alinment
(e.g. somewhat specialized cross-correlation)
IMOD: tiltxcorr


Finer alignment, by one of:

  • alignment using fiducial model (fiducials are small high-contrast things, typically gold beads)
  • fiducialless alignment, e.g. patch tracking / feature tracking
  • skipping (effectively assumes rough alignment is enough, which it basically never is)


model/correct CTF (optional)

only really required for higher resolution, which you may not need


remove fiducial markers from images

would be disturbing influence in tomogram


filtering


make tomogram from the stack

  • e.g. (Weighted) BackProjection (WBP), or SIRT (Simultaneous Iterative Reconstruction Technique)


slice out just the specimen (optional, but rather practical)

Optional: noise reduction via NAD (nonlinear anisotropic diffusion) filter


Where applicable: combine dual axis tomogram


Where useful: Subvolume averaging

if you have multiple of the same thing within a tomogram that you want to combine (sort of single particle style)



Notes:

  • Fiducial tracking can be done by manually telling it which correspond, or doing it via IMOD, or RAPTOR, or other.
Doing fine-detail alignment with fiducials is a nontrivial optimization problem.
Using more makes for finer detail in the alignment (averages and noise),
but also requires and kicking out the ones that seem to disagree with the consensus,
because a few bad cases would throw off otherwise detailed averages.
IMOD: imodfindbeads, autofidseed, others
  • IMOD goes to 3D twice, first for something to work on, later for a cleaned version. There seem to be a few reasons for this.

(semi)automated

Etomo runs you through the steps with some interaction in each.


batchruntomo is essentially a job manager

you give it directive files (adocs)
...with pre-set steps; you can run parts at a time (see -start, -end), useful for inspection before you continue, and to redo things with different parameters.

The list of directives: https://bio3d.colorado.edu/imod/doc/directives.html

Directives are sorted into:

  • setupset - mostly describes collection and dataset
  • com-param - parameters for programs (like those in .com files)
  • run-time - parameters interpreted by batchruntomo or etomo (verify)

Unsorted

PEET (Particle Estimation for Electron Tomography) [1]


RAPTOR (Robust Alignment and Projection Estimation for Tomographic Reconstruction) used to be separate, and is now integrated, and a more automatic alternative. [2]