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<p>Dear Prof. Rubinstein,</p>
<p>EMAN2 does this quite nicely, a quick description is found at</p>
<p><span style="color:rgb(33,33,33); font-size:13.3333px"><a href="http://blake.bcm.edu/emanwiki/EMAN2ImageFormats#Region_I.2FO" class="x_OWAAutoLink" id="LPlnk181759">http://blake.bcm.edu/emanwiki/EMAN2ImageFormats#Region_I.2FO</a><br>
</span></p>
<p><span style="color:rgb(33,33,33); font-size:13.3333px">One specifies a "Region" object and then this is supplied as an argument to the read_image function (or several other functions). </span></p>
<p><span style="color:rgb(33,33,33); font-size:13.3333px">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.</span></p>
<p><span style="color:rgb(33,33,33); font-size:13.3333px">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.</span></p>
<p><span style="color:rgb(33,33,33); font-size:13.3333px">Sincerely,</span></p>
<p><span style="color:rgb(33,33,33); font-size:13.3333px">Jason Kaelber</span></p>
<p><span style="color:rgb(33,33,33); font-size:13.3333px">National Center for Macromolecular Imaging</span></p>
<p><font color="#212121"><span style="font-size:13.3333px">Baylor College of Medicine</span></font></p>
<p><span style="color:rgb(33,33,33); font-size:13.3333px"><br>
</span></p>
<p><span style="color:rgb(33,33,33); font-size:13.3333px">Message: 3</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">Date: Fri, 15 Jul 2016 17:24:16 -0400</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">From: john.rubinstein@utoronto.ca</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">To: 3dem@ncmir.ucsd.edu</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">Subject: [3dem] Python function equivalent to MRC image2010 Irdpas</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">Message-ID: <20160715172416.44exnemqqok0sk40@webmail.utoronto.ca></span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px"> format="flowed"</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">Dear Colleagues,</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">In order to save some coding, I am hoping that someone can point me to </span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">a Python function that is equivalent the MRC Image2010 subroutine </span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">Irdpas, which reads part of a section from an MRC format image stack. </span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">That is, I would like to specify a z-slice, a start point in x, an end </span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">point in x, a start point in y, and an end point in y, and have the </span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">function return a 2D array that contains the relevant portion of the </span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">specified slice. Any python code that extracts particles from movies </span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">should have this function. A more general function that extracts a </span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">volume from the stack/volume would also be great.</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">Thanks in advance for any suggestions.</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">Best regards,</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">John</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">-- </span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">John Rubinstein</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">Molecular Structure and Function Program</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">The Hospital for Sick Children Research Institute</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">686 Bay Street, Rm. 20-9705</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">Toronto, ON</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">Canada</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">M5G 0A4</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">Tel: (+001) 416-813-7255</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">Fax: (+001) 416-813-5022</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<a href="http://www.sickkids.ca/research/rubinstein" target="_blank" style="font-size:13.3333px">www.sickkids.ca/research/rubinstein</a><br>
</p>
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<b>Sent:</b> Saturday, July 16, 2016 2:00:01 PM<br>
<b>To:</b> 3dem@ncmir.ucsd.edu<br>
<b>Subject:</b> 3dem Digest, Vol 107, Issue 15</font>
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Today's Topics:<br>
<br>
1. Vitrobot blotting on one side only? (Garry P Morgan)<br>
2. Re: Vitrobot blotting on one side only? (Ben Engel)<br>
3. Python function equivalent to MRC image2010 Irdpas<br>
(john.rubinstein@utoronto.ca)<br>
4. Re: Python function equivalent to MRC image2010 Irdpas<br>
(Jose Miguel de la Rosa Trevin)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 15 Jul 2016 19:56:08 +0000<br>
From: Garry P Morgan <Garry.Morgan@Colorado.EDU><br>
To: "3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu><br>
Subject: [3dem] Vitrobot blotting on one side only?<br>
Message-ID: <5042440C-2ABE-4B4B-A75F-9ECD9EE3AAA9@colorado.edu><br>
Content-Type: text/plain; charset="Windows-1252"<br>
<br>
Hello,<br>
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.<br>
thanks,<br>
Garry<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Fri, 15 Jul 2016 13:03:13 -0700<br>
From: Ben Engel <bdengel@gmail.com><br>
To: Garry P Morgan <Garry.Morgan@colorado.edu><br>
Cc: "3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu><br>
Subject: Re: [3dem] Vitrobot blotting on one side only?<br>
Message-ID:<br>
<CAC-vZ1hshVb2x+PZBmQ5OX0+qn-J0rrs7oyC2CXS+Q8C5ZUBfg@mail.gmail.com><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Garry,<br>
<br>
We routinely blot from one side with the Vitrobot when vitrifying cells.<br>
On the side without the filter paper, we put a teflon sheet that is cut in<br>
the same shape. Some of us also put a second piece of teflon under the<br>
filter paper to slow the blotting, but I am not sure how necessary that is.<br>
<br>
Best,<br>
Ben<br>
<br>
On Fri, Jul 15, 2016 at 12:56 PM, Garry P Morgan <Garry.Morgan@colorado.edu><br>
wrote:<br>
<br>
> Hello,<br>
> I?d like to blot with only one filter paper on the Vitrobot. Has anyone<br>
> done this successfully? If you have any tips or tricks could you please<br>
> let me know? I was thinking of using a piece of aclar film in place of the<br>
> filter paper on the non-blotting side. I?m sure there are other approaches.<br>
> Any advice would be appreciated.<br>
> thanks,<br>
> Garry<br>
><br>
> _______________________________________________<br>
> 3dem mailing list<br>
> 3dem@ncmir.ucsd.edu<br>
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Message: 3<br>
Date: Fri, 15 Jul 2016 17:24:16 -0400<br>
From: john.rubinstein@utoronto.ca<br>
To: 3dem@ncmir.ucsd.edu<br>
Subject: [3dem] Python function equivalent to MRC image2010 Irdpas<br>
Message-ID: <20160715172416.44exnemqqok0sk40@webmail.utoronto.ca><br>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";<br>
format="flowed"<br>
<br>
Dear Colleagues,<br>
<br>
In order to save some coding, I am hoping that someone can point me to <br>
a Python function that is equivalent the MRC Image2010 subroutine <br>
Irdpas, which reads part of a section from an MRC format image stack. <br>
That is, I would like to specify a z-slice, a start point in x, an end <br>
point in x, a start point in y, and an end point in y, and have the <br>
function return a 2D array that contains the relevant portion of the <br>
specified slice. Any python code that extracts particles from movies <br>
should have this function. A more general function that extracts a <br>
volume from the stack/volume would also be great.<br>
<br>
Thanks in advance for any suggestions.<br>
<br>
Best regards,<br>
John<br>
<br>
-- <br>
John Rubinstein<br>
Molecular Structure and Function Program<br>
The Hospital for Sick Children Research Institute<br>
686 Bay Street, Rm. 20-9705<br>
Toronto, ON<br>
Canada<br>
M5G 0A4<br>
Tel: (+001) 416-813-7255<br>
Fax: (+001) 416-813-5022<br>
<a href="http://www.sickkids.ca/research/rubinstein">www.sickkids.ca/research/rubinstein</a><br>
<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Sat, 16 Jul 2016 00:18:29 +0200<br>
From: Jose Miguel de la Rosa Trevin <jmdelarosa@cnb.csic.es><br>
To: John Rubinstein <john.rubinstein@utoronto.ca><br>
Cc: 3dem@ncmir.ucsd.edu<br>
Subject: Re: [3dem] Python function equivalent to MRC image2010 Irdpas<br>
Message-ID:<br>
<CAGhngE2AYkF1FY-7Gm-CwE=SDSnZr6iVyQzhw6oyr3iL5fj=ew@mail.gmail.com><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear John,<br>
<br>
In Scipion we have an ImageHandler class that can be used to read/write<br>
images/volumes inside stacks or in individual files.<br>
After reading the image, there is a function getData that return a numpy<br>
array that is very flexible in terms of indexing (which can be used for<br>
cropping/extracting particles/volumes).<br>
<br>
Recently we were integrating the Localized Reconstruction with Juha<br>
Huiskonen and we develop a simple protocol to extract the subparticles from<br>
the particles images. The code may serve to illustrate the usage of this<br>
classes and its potential.<br>
<br>
<a href="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=">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=</a>
<br>
<br>
The main downside is that you need to install the whole Scipion framework<br>
for just one desired Python function, which I understand that you will<br>
prefer to be a self-contained independent function.<br>
<br>
Hope this helps,<br>
Kind regards,<br>
Jose Miguel.<br>
<br>
<br>
On Fri, Jul 15, 2016 at 11:24 PM, <john.rubinstein@utoronto.ca> wrote:<br>
<br>
> Dear Colleagues,<br>
><br>
> In order to save some coding, I am hoping that someone can point me to a<br>
> Python function that is equivalent the MRC Image2010 subroutine Irdpas,<br>
> which reads part of a section from an MRC format image stack. That is, I<br>
> would like to specify a z-slice, a start point in x, an end point in x, a<br>
> start point in y, and an end point in y, and have the function return a 2D<br>
> array that contains the relevant portion of the specified slice. Any python<br>
> code that extracts particles from movies should have this function. A more<br>
> general function that extracts a volume from the stack/volume would also be<br>
> great.<br>
><br>
> Thanks in advance for any suggestions.<br>
><br>
> Best regards,<br>
> John<br>
><br>
> --<br>
> John Rubinstein<br>
> Molecular Structure and Function Program<br>
> The Hospital for Sick Children Research Institute<br>
> 686 Bay Street, Rm. 20-9705<br>
> Toronto, ON<br>
> Canada<br>
> M5G 0A4<br>
> Tel: (+001) 416-813-7255<br>
> Fax: (+001) 416-813-5022<br>
> <a href="http://www.sickkids.ca/research/rubinstein">www.sickkids.ca/research/rubinstein</a><br>
><br>
><br>
><br>
> _______________________________________________<br>
> 3dem mailing list<br>
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