[3dem] 3dem Digest, Vol 107, Issue 15
John Rubinstein
john.rubinstein at utoronto.ca
Sun Jul 17 19:20:21 PDT 2016
Thanks very much, Jason.
This sounds great - I'll have a look at the code.
Best wishes,
John
--
Sent from my mobile device, please excuse typos
On Jul 17, 2016, 4:58 PM, at 4:58 PM, "Kaelber, Jason Toye" <kaelber at bcm.edu> wrote:
>Dear Prof. Rubinstein,
>
>EMAN2 does this quite nicely, a quick description is found at
>
>http://blake.bcm.edu/emanwiki/EMAN2ImageFormats#Region_I.2FO
>
>One specifies a "Region" object and then this is supplied as an
>argument to the read_image function (or several other functions).
>
>If you have an entire file in memory as an EMData object and want to
>dice it up, the EMData.get_clip(Region) function is what you are
>looking for.
>
>The EMData object also has a function numpy() that outputs the image as
>a Numpy array that may make it easier to interface with your existing
>project.
>
>Sincerely,
>
>Jason Kaelber
>
>National Center for Macromolecular Imaging
>
>Baylor College of Medicine
>
>
>Message: 3
>Date: Fri, 15 Jul 2016 17:24:16 -0400
>From: john.rubinstein at utoronto.ca
>To: 3dem at ncmir.ucsd.edu
>Subject: [3dem] Python function equivalent to MRC image2010 Irdpas
>Message-ID: <20160715172416.44exnemqqok0sk40 at webmail.utoronto.ca>
>Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
>Dear Colleagues,
>
>In order to save some coding, I am hoping that someone can point me to
>a Python function that is equivalent the MRC Image2010 subroutine
>Irdpas, which reads part of a section from an MRC format image stack.
>That is, I would like to specify a z-slice, a start point in x, an end
>point in x, a start point in y, and an end point in y, and have the
>function return a 2D array that contains the relevant portion of the
>specified slice. Any python code that extracts particles from movies
>should have this function. A more general function that extracts a
>volume from the stack/volume would also be great.
>
>Thanks in advance for any suggestions.
>
>Best regards,
>John
>
>--
>John Rubinstein
>Molecular Structure and Function Program
>The Hospital for Sick Children Research Institute
>686 Bay Street, Rm. 20-9705
>Toronto, ON
>Canada
>M5G 0A4
>Tel: (+001) 416-813-7255
>Fax: (+001) 416-813-5022
>www.sickkids.ca/research/rubinstein<http://www.sickkids.ca/research/rubinstein>
>
>________________________________
>From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of
>3dem-request at ncmir.ucsd.edu <3dem-request at ncmir.ucsd.edu>
>Sent: Saturday, July 16, 2016 2:00:01 PM
>To: 3dem at ncmir.ucsd.edu
>Subject: 3dem Digest, Vol 107, Issue 15
>
>***CAUTION:*** This email is not from a BCM Source. Only click links
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>
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>Today's Topics:
>
> 1. Vitrobot blotting on one side only? (Garry P Morgan)
> 2. Re: Vitrobot blotting on one side only? (Ben Engel)
> 3. Python function equivalent to MRC image2010 Irdpas
> (john.rubinstein at utoronto.ca)
> 4. Re: Python function equivalent to MRC image2010 Irdpas
> (Jose Miguel de la Rosa Trevin)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Fri, 15 Jul 2016 19:56:08 +0000
>From: Garry P Morgan <Garry.Morgan at Colorado.EDU>
>To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
>Subject: [3dem] Vitrobot blotting on one side only?
>Message-ID: <5042440C-2ABE-4B4B-A75F-9ECD9EE3AAA9 at colorado.edu>
>Content-Type: text/plain; charset="Windows-1252"
>
>Hello,
>I?d like to blot with only one filter paper on the Vitrobot. Has
>anyone done this successfully? If you have any tips or tricks could
>you please let me know? I was thinking of using a piece of aclar film
>in place of the filter paper on the non-blotting side. I?m sure there
>are other approaches. Any advice would be appreciated.
>thanks,
>Garry
>
>
>
>------------------------------
>
>Message: 2
>Date: Fri, 15 Jul 2016 13:03:13 -0700
>From: Ben Engel <bdengel at gmail.com>
>To: Garry P Morgan <Garry.Morgan at colorado.edu>
>Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
>Subject: Re: [3dem] Vitrobot blotting on one side only?
>Message-ID:
> <CAC-vZ1hshVb2x+PZBmQ5OX0+qn-J0rrs7oyC2CXS+Q8C5ZUBfg at mail.gmail.com>
>Content-Type: text/plain; charset="utf-8"
>
>Hi Garry,
>
>We routinely blot from one side with the Vitrobot when vitrifying
>cells.
>On the side without the filter paper, we put a teflon sheet that is cut
>in
>the same shape. Some of us also put a second piece of teflon under
>the
>filter paper to slow the blotting, but I am not sure how necessary that
>is.
>
>Best,
>Ben
>
>On Fri, Jul 15, 2016 at 12:56 PM, Garry P Morgan
><Garry.Morgan at colorado.edu>
>wrote:
>
>> Hello,
>> I?d like to blot with only one filter paper on the Vitrobot. Has
>anyone
>> done this successfully? If you have any tips or tricks could you
>please
>> let me know? I was thinking of using a piece of aclar film in place
>of the
>> filter paper on the non-blotting side. I?m sure there are other
>approaches.
>> Any advice would be appreciated.
>> thanks,
>> Garry
>>
>> _______________________________________________
>> 3dem mailing list
>> 3dem at ncmir.ucsd.edu
>>
>https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DQICAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=uK-VlaB2SqducnRahrFQHA&m=jG5E6YVxXEdQrMsZcUtaAPQXgOTeNGO9BDJrb-i1EBY&s=mc5Nw0yDZJuAnqVN43oYLn7Zr1NrdJjhJWAse9q_Xko&e=
>>
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>------------------------------
>
>Message: 3
>Date: Fri, 15 Jul 2016 17:24:16 -0400
>From: john.rubinstein at utoronto.ca
>To: 3dem at ncmir.ucsd.edu
>Subject: [3dem] Python function equivalent to MRC image2010 Irdpas
>Message-ID: <20160715172416.44exnemqqok0sk40 at webmail.utoronto.ca>
>Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
>Dear Colleagues,
>
>In order to save some coding, I am hoping that someone can point me to
>a Python function that is equivalent the MRC Image2010 subroutine
>Irdpas, which reads part of a section from an MRC format image stack.
>That is, I would like to specify a z-slice, a start point in x, an end
>point in x, a start point in y, and an end point in y, and have the
>function return a 2D array that contains the relevant portion of the
>specified slice. Any python code that extracts particles from movies
>should have this function. A more general function that extracts a
>volume from the stack/volume would also be great.
>
>Thanks in advance for any suggestions.
>
>Best regards,
>John
>
>--
>John Rubinstein
>Molecular Structure and Function Program
>The Hospital for Sick Children Research Institute
>686 Bay Street, Rm. 20-9705
>Toronto, ON
>Canada
>M5G 0A4
>Tel: (+001) 416-813-7255
>Fax: (+001) 416-813-5022
>www.sickkids.ca/research/rubinstein<http://www.sickkids.ca/research/rubinstein>
>
>
>
>
>
>------------------------------
>
>Message: 4
>Date: Sat, 16 Jul 2016 00:18:29 +0200
>From: Jose Miguel de la Rosa Trevin <jmdelarosa at cnb.csic.es>
>To: John Rubinstein <john.rubinstein at utoronto.ca>
>Cc: 3dem at ncmir.ucsd.edu
>Subject: Re: [3dem] Python function equivalent to MRC image2010 Irdpas
>Message-ID:
> <CAGhngE2AYkF1FY-7Gm-CwE=SDSnZr6iVyQzhw6oyr3iL5fj=ew at mail.gmail.com>
>Content-Type: text/plain; charset="utf-8"
>
>Dear John,
>
>In Scipion we have an ImageHandler class that can be used to read/write
>images/volumes inside stacks or in individual files.
>After reading the image, there is a function getData that return a
>numpy
>array that is very flexible in terms of indexing (which can be used for
>cropping/extracting particles/volumes).
>
>Recently we were integrating the Localized Reconstruction with Juha
>Huiskonen and we develop a simple protocol to extract the subparticles
>from
>the particles images. The code may serve to illustrate the usage of
>this
>classes and its potential.
>
>https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_I2PC_scipion_blob_devel-2Dlocalized-2Drecons_pyworkflow_em_packages_opic_protocol-5Flocalized-5Fextraction.py-23L97&d=DQICAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=uK-VlaB2SqducnRahrFQHA&m=jG5E6YVxXEdQrMsZcUtaAPQXgOTeNGO9BDJrb-i1EBY&s=vkCOFWljw4ImreOL9S8X36_t2GaiG1QgbUhQfXn0YWs&e=
>
>The main downside is that you need to install the whole Scipion
>framework
>for just one desired Python function, which I understand that you will
>prefer to be a self-contained independent function.
>
>Hope this helps,
>Kind regards,
>Jose Miguel.
>
>
>On Fri, Jul 15, 2016 at 11:24 PM, <john.rubinstein at utoronto.ca> wrote:
>
>> Dear Colleagues,
>>
>> In order to save some coding, I am hoping that someone can point me
>to a
>> Python function that is equivalent the MRC Image2010 subroutine
>Irdpas,
>> which reads part of a section from an MRC format image stack. That
>is, I
>> would like to specify a z-slice, a start point in x, an end point in
>x, a
>> start point in y, and an end point in y, and have the function return
>a 2D
>> array that contains the relevant portion of the specified slice. Any
>python
>> code that extracts particles from movies should have this function. A
>more
>> general function that extracts a volume from the stack/volume would
>also be
>> great.
>>
>> Thanks in advance for any suggestions.
>>
>> Best regards,
>> John
>>
>> --
>> John Rubinstein
>> Molecular Structure and Function Program
>> The Hospital for Sick Children Research Institute
>> 686 Bay Street, Rm. 20-9705
>> Toronto, ON
>> Canada
>> M5G 0A4
>> Tel: (+001) 416-813-7255
>> Fax: (+001) 416-813-5022
>>
>www.sickkids.ca/research/rubinstein<http://www.sickkids.ca/research/rubinstein>
>>
>>
>>
>> _______________________________________________
>> 3dem mailing list
>> 3dem at ncmir.ucsd.edu
>>
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>>
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