[3dem] 3dem Digest, Vol 107, Issue 15

Kaelber, Jason Toye kaelber at bcm.edu
Sun Jul 17 13:58:41 PDT 2016


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
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Subject: 3dem Digest, Vol 107, Issue 15

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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
> 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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