[3dem] CTF in tilted image
Benjamin Himes
himes.benjamin at gmail.com
Mon Feb 28 16:46:26 PST 2022
Both emClarity and cisTEM (recent alpha version) implement an algorithm
that also tiles an image of a tilted specimen, but stretches the off-axis
power-spectra in such a way that the Thon rings add more-or-less coherently.
In emClarity, this is based of the tilt-series alignment.
In cisTEM, the tilt-axis-angle and tilt-angle are fit as a part of the
tilted CTF refinement.
The basic algorithm is described in my thesis (online at Pitt med) and I
believe in the emClarity Nat Meth. paper.
Here's a movie
<https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_cryo2go_status_1282036490378280961-3Fs-3D20-26t-3Dkg1qVYhpGcqQa5z3qyAFAg&d=DwIFaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=1ewdSi1Sw81zQt6Nq3CrsySs-Y287rlAiec-bqJlfPLyQA_vi_KKJ1zxdz-nyZxB&s=uOWrwyCyn0SHh3IdOd5dnzsno3epRK-16lKliqKBnsc&e= >of
what that looks like in emClarity.
You can find some developmental versions of cisTEM and docs here
<https://urldefense.proofpoint.com/v2/url?u=https-3A__bhimes.github.io_cisTEM-5Fdocs_docs_sim_tutorials_tutorials.html&d=DwIFaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=1ewdSi1Sw81zQt6Nq3CrsySs-Y287rlAiec-bqJlfPLyQA_vi_KKJ1zxdz-nyZxB&s=1I6nf3WKHJ4CgOEGj0gCGld5hh3dYr6xMs5vpLf_8C4&e= >.
HTH
Ben
------------------------
Benjamin A. Himes, PhD
Computer Vision Specialist
Grigorieff Lab
HHMI, RNA Therapeutics Institute, University of Massachusetts Medical School
AS.5 2041
774-455-3690
Visual Proteomics @ cisTEM <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_timothygrant80_cisTEM&d=DwIFaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=1ewdSi1Sw81zQt6Nq3CrsySs-Y287rlAiec-bqJlfPLyQA_vi_KKJ1zxdz-nyZxB&s=41KwSGC4luYRkhhe2QfAgeOzeUz_blD009ZucnyZwNM&e= >
cryo-STA development @ emClarity <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bHimes_emClarity&d=DwIFaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=1ewdSi1Sw81zQt6Nq3CrsySs-Y287rlAiec-bqJlfPLyQA_vi_KKJ1zxdz-nyZxB&s=Mr28B9czdsoEDTAJoaNMQmJ9M8dSaufB3EUr8LRt_D4&e= >
------------------------
On Mon, Feb 28, 2022 at 6:07 PM <3dem-request at ncmir.ucsd.edu> wrote:
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> Today's Topics:
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> 1. tilted transfer functions? (Morgan, David Gene)
> 2. Re: tilted transfer functions? (Daniel Asarnow)
> 3. Re: [External] Re: tilted transfer functions?
> (Morgan, David Gene)
> 4. Re: [External] Re: tilted transfer functions?
> (Michael Radermacher)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 28 Feb 2022 22:41:31 +0000
> From: "Morgan, David Gene" <dagmorga at indiana.edu>
> To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Subject: [3dem] tilted transfer functions?
> Message-ID:
> <
> MWHPR08MB2640E93081D1A4936344921FD0019 at MWHPR08MB2640.namprd08.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> What's the best way to evaluate the CTF of an image that has a significant
> amount of tilt?
>
> --
> politics is more difficult than physics.
> A. Einstein
>
> David Gene Morgan
> Electron Microscopy Center
> 047E Simon Hall
> IU Bloomington
> 812 856 1457 (office)
> 812 856 3221 (3200)
>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__iubemcenter.indiana.edu&d=DwIFAw&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=o5hWD3mEM1CnBQcA1CoCbNa2ZHuekOPBxJopTggUSnV5bTDS_itRzHiJgm-MqSkZ&s=fCFZWGmlhcc6nzBlB6MWW5ml9YVPIK3FHs7zbhuCqIs&e=
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> Message: 2
> Date: Mon, 28 Feb 2022 14:45:38 -0800
> From: Daniel Asarnow <asarnow at msg.ucsf.edu>
> To: "Morgan, David Gene" <dagmorga at indiana.edu>
> Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Subject: Re: [3dem] tilted transfer functions?
> Message-ID:
> <
> CALiNCbYfNgD2yzrvMxn6Biiu8Ea6X9+U+c20qHF3+dfMTrzn4Q at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> I think any patch-based CTF program, like the one in cryosparc or gCTF's
> local mode (with evenly spaced coordinates instead of real particle
> locations) would work well. With cryoSPARC there's an easy method to plot
> the tilt axis; you can also choose a specific number X and Y divisions for
> the patches.
>
> Best,
> -da
>
> On Mon, Feb 28, 2022 at 2:41 PM Morgan, David Gene <dagmorga at indiana.edu>
> wrote:
>
> > Hi,
> >
> > What's the best way to evaluate the CTF of an image that has a
> significant
> > amount of tilt?
> >
> > --
> > politics is more difficult than physics.
> > A. Einstein
> >
> > David Gene Morgan
> > Electron Microscopy Center
> > 047E Simon Hall
> > IU Bloomington
> > 812 856 1457 (office)
> > 812 856 3221 (3200)
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__iubemcenter.indiana.edu&d=DwIFaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=HH1ykW6tLwgxKgan8Zd6LycpIki40sPo8vvB68LicICQO8KjnJ4KcbS9olx30LkL&s=LvXJmrsSwPkhXWH7WRotXfrp1kAUUBMSB-JXiciGOlg&e=
> > <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__iubemcenter.indiana.edu&d=DwQFAw&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=o5hWD3mEM1CnBQcA1CoCbNa2ZHuekOPBxJopTggUSnV5bTDS_itRzHiJgm-MqSkZ&s=fCFZWGmlhcc6nzBlB6MWW5ml9YVPIK3FHs7zbhuCqIs&e=
> >
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> ------------------------------
>
> Message: 3
> Date: Mon, 28 Feb 2022 22:50:32 +0000
> From: "Morgan, David Gene" <dagmorga at indiana.edu>
> To: Daniel Asarnow <asarnow at msg.ucsf.edu>
> Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Subject: Re: [3dem] [External] Re: tilted transfer functions?
> Message-ID:
> <
> MWHPR08MB26405A3E3B47067BC7C8A18CD0019 at MWHPR08MB2640.namprd08.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="us-ascii"
>
> Daniel,
>
> The problem is that the tilt causes the higher resolution Thon rings to
> become out-of-phase, and so the standard programs can't give a decent
> estimate of the goodness of-fit. I vaguely remember that someone had a
> program that took the tilt into account a number of years ago, but a quick
> hunt for it didn't turn up anything.
>
> --
> politics is more difficult than physics.
> A. Einstein
>
> David Gene Morgan
> Electron Microscopy Center
> 047E Simon Hall
> IU Bloomington
> 812 856 1457 (office)
> 812 856 3221 (3200)
>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__iubemcenter.indiana.edu&d=DwIFAg&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=XfGX1GAOnfj3mLhTnyN8uolpwG3BMtMXZYm0H1sLXZy6LYulpNRf8T8jKuxWTOju&s=qBVmiqzIFHPhsmMv2GVKS3tE0Y3k35YCkiZM5CmZ2cg&e=
> ________________________________
> From: Daniel Asarnow <asarnow at msg.ucsf.edu>
> Sent: Monday, February 28, 2022 5:45 PM
> To: Morgan, David Gene <dagmorga at indiana.edu>
> Cc: 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
> Subject: [External] Re: [3dem] tilted transfer functions?
>
> This message was sent from a non-IU address. Please exercise caution when
> clicking links or opening attachments from external sources.
>
> I think any patch-based CTF program, like the one in cryosparc or gCTF's
> local mode (with evenly spaced coordinates instead of real particle
> locations) would work well. With cryoSPARC there's an easy method to plot
> the tilt axis; you can also choose a specific number X and Y divisions for
> the patches.
>
> Best,
> -da
>
> On Mon, Feb 28, 2022 at 2:41 PM Morgan, David Gene <dagmorga at indiana.edu
> <mailto:dagmorga at indiana.edu>> wrote:
> Hi,
>
> What's the best way to evaluate the CTF of an image that has a significant
> amount of tilt?
>
> --
> politics is more difficult than physics.
> A. Einstein
>
> David Gene Morgan
> Electron Microscopy Center
> 047E Simon Hall
> IU Bloomington
> 812 856 1457 (office)
> 812 856 3221 (3200)
>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__iubemcenter.indiana.edu&d=DwIFAg&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=XfGX1GAOnfj3mLhTnyN8uolpwG3BMtMXZYm0H1sLXZy6LYulpNRf8T8jKuxWTOju&s=qBVmiqzIFHPhsmMv2GVKS3tE0Y3k35YCkiZM5CmZ2cg&e=
> <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__iubemcenter.indiana.edu&d=DwQFAw&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=o5hWD3mEM1CnBQcA1CoCbNa2ZHuekOPBxJopTggUSnV5bTDS_itRzHiJgm-MqSkZ&s=fCFZWGmlhcc6nzBlB6MWW5ml9YVPIK3FHs7zbhuCqIs&e=
> >
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
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> Message: 4
> Date: Tue, 1 Mar 2022 00:07:14 +0100
> From: Michael Radermacher <Michael.Radermacher at uvm.edu>
> To: 3dem at ncmir.ucsd.edu
> Subject: Re: [3dem] [External] Re: tilted transfer functions?
> Message-ID: <cf80c020-6b03-0b4b-65f0-6843eebda42a at uvm.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> David, Daniel
>
> The tilt can be taken into account as described in the CTF correction
> section of the paper on the 3D reconstruction of the V1 ATPase:
> Journal of Structural Biology, 135 (2001), 26-37, Materials and Methods.
> May be this is what you are referring to.
>
> Essentially you divide the tilt image into equal patches, determine the
> CTF for each patch, then fit a plane to the CTF values found. The
> equation of this plane then can be used to determine the CTF values of
> each boxed out particle based on its location in the large image, and
> correct the CTF individually.
> --
> _______________
> Michael Radermacher, PhD, Prof. Emeritus, FMSA
> University of Vermont
> Dept. Molecular Physiology and Biophysics
> Burlington, VT 05405
> Website:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.uvm.edu_-7Emraderma&d=DwID-g&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=5uPib0OSWzEoaC0FE9wYbrgH7TPwpu6dKsmumyxY1p9PNH8Of-IyLYZ_fILF77zA&s=RCyh812VLtPhQ4JFmv5Qr9jPwbc5U0QbEWuVlbQw3VM&e=
>
> On 2/28/22 11:50 PM, Morgan, David Gene wrote:
> > Daniel,
> >
> > The problem is that the tilt causes the higher resolution Thon rings to
> > become out-of-phase, and so the standard programs can't give a decent
> > estimate of the goodness of-fit.? I vaguely remember that someone had a
> > program that took the tilt into account a number of years ago, but a
> > quick hunt for it didn't turn up anything.
> >
> > --
> > ? ? politics is more difficult than physics.
> > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?A. Einstein
> >
> > ??????????? David Gene Morgan
> > ??????? Electron Microscopy Center
> > ???????????? 047E Simon Hall
> > ???????????? IU Bloomington
> > ????????? 812 856 1457 (office)
> > ????????? 812 856 3221 (3200)
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__iubemcenter.indiana.edu&d=DwID-g&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=5uPib0OSWzEoaC0FE9wYbrgH7TPwpu6dKsmumyxY1p9PNH8Of-IyLYZ_fILF77zA&s=UAqpQCAtEmUAe-IDHFHuBqLW1x5Q8oNyz08NmP620YM&e=
>
> > <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__iubemcenter.indiana.edu&d=DwQFAg&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=XfGX1GAOnfj3mLhTnyN8uolpwG3BMtMXZYm0H1sLXZy6LYulpNRf8T8jKuxWTOju&s=qBVmiqzIFHPhsmMv2GVKS3tE0Y3k35YCkiZM5CmZ2cg&e=
> >
> > ------------------------------------------------------------------------
> > *From:* Daniel Asarnow <asarnow at msg.ucsf.edu>
> > *Sent:* Monday, February 28, 2022 5:45 PM
> > *To:* Morgan, David Gene <dagmorga at indiana.edu>
> > *Cc:* 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
> > *Subject:* [External] Re: [3dem] tilted transfer functions?
> > This message was sent from a non-IU address. Please exercise caution
> > when clicking links or opening attachments from external sources.
> >
> > I think any patch-based CTF program, like the one in cryosparc or gCTF's
> > local mode (with evenly spaced coordinates instead of real particle
> > locations) would work well. With cryoSPARC there's an easy method to
> > plot the tilt axis; you can also choose a specific number X and Y
> > divisions for the patches.
> >
> > Best,
> > -da
> >
> > On Mon, Feb 28, 2022 at 2:41 PM Morgan, David Gene <dagmorga at indiana.edu
> > <mailto:dagmorga at indiana.edu>> wrote:
> >
> > Hi,
> >
> > What's the best way to evaluate the CTF of an image that has a
> > significant amount of tilt?
> >
> > --
> > ? ? politics is more difficult than physics.
> > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?A. Einstein
> >
> > ??????????? David Gene Morgan
> > ??????? Electron Microscopy Center
> > ???????????? 047E Simon Hall
> > ???????????? IU Bloomington
> > ????????? 812 856 1457 (office)
> > ????????? 812 856 3221 (3200)
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__iubemcenter.indiana.edu&d=DwID-g&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=5uPib0OSWzEoaC0FE9wYbrgH7TPwpu6dKsmumyxY1p9PNH8Of-IyLYZ_fILF77zA&s=UAqpQCAtEmUAe-IDHFHuBqLW1x5Q8oNyz08NmP620YM&e=
> > <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__iubemcenter.indiana.edu&d=DwQFAw&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=o5hWD3mEM1CnBQcA1CoCbNa2ZHuekOPBxJopTggUSnV5bTDS_itRzHiJgm-MqSkZ&s=fCFZWGmlhcc6nzBlB6MWW5ml9YVPIK3FHs7zbhuCqIs&e=
> >
> > _______________________________________________
> > 3dem mailing list
> > 3dem at ncmir.ucsd.edu <mailto:3dem at ncmir.ucsd.edu>
> > https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
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> >
> >
> > _______________________________________________
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> > 3dem at ncmir.ucsd.edu
> > https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
> >
>
> --
> _______________
> Michael Radermacher, PhD, Prof. Emeritus, FMSA
> University of Vermont
> Dept. Molecular Physiology and Biophysics
> Burlington, VT 05405
> Website:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.uvm.edu_-7Emraderma&d=DwID-g&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=5uPib0OSWzEoaC0FE9wYbrgH7TPwpu6dKsmumyxY1p9PNH8Of-IyLYZ_fILF77zA&s=RCyh812VLtPhQ4JFmv5Qr9jPwbc5U0QbEWuVlbQw3VM&e=
>
>
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>
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