[3dem] 3dem Digest, EMI to MRC
William Nicolas
wjnicolas at hotmail.com
Fri Mar 14 00:54:51 PDT 2014
Dear Xiaodong Yen,
I have a imageJ plugin that converts SER files (which are normally created simultaneously with the .emi file) in TIFF files. It’s more exactly a macro in which you point out the folder where all your .ser files are and opens/converts them all.
If you are interested I can forward you the email of my colleague that developed that useful little macro
Best regards,
William Nicolas, PhD
Le 14 mars 2014 à 05:32, 3dem-request at ncmir.ucsd.edu a écrit :
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> Today's Topics:
>
> 1. Re: Virus on Carbon (Xinghong Dai)
> 2. Re: Virus on Carbon (C.J.)
> 3. Re: EMI to MRC image format conversion (Xiaodong Yan)
> 4. Re: EMI to MRC image format conversion (Steven Ludtke)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 13 Mar 2014 21:16:31 -0700
> From: "Xinghong Dai" <bestdz at gmail.com>
> To: 'Luiza Mendon?a' <luiza at caltech.edu>, "'3DEM Mailing List'"
> <3dem at ncmir.ucsd.edu>
> Subject: Re: [3dem] Virus on Carbon
> Message-ID: <004601cf3f3c$2f004c10$8d00e430$@com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Luiza,
>
> Maybe you can try to make the ice a little bit thicker to see if that will make any difference. They theory is that, if the ice is too thin, big particles will not stay in the hole due to size exclusion effect. I had similar situation when working with big viruses.
>
> Good luck!
>
>
>
> Xinghong
>
>
>
>
>
> ???: 3dem-bounces at ncmir.ucsd.edu [mailto:3dem-bounces at ncmir.ucsd.edu] ?? Luiza Mendon?a
> ????: Thursday, March 13, 2014 4:41 PM
> ???: 3DEM Mailing List
> ??: [3dem] Virus on Carbon
>
>
>
> Dear colleagues,
>
>
>
> I work with HIV particles and (at least in my samples), they like the carbon film on the grids much better than the holes, but for me this is a big problem, as, even using high titer preps, they rarely go to the holes, resulting in less-than-perfect tomograms. Has anyone else had this problem? What did you do to solve it?
>
> My particles are resusspended in PBS (with gold fiducials) at the time of freezing.
>
>
>
> Best,
>
> Luiza.
>
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> ------------------------------
>
> Message: 2
> Date: Fri, 14 Mar 2014 12:23:24 +0800
> From: "C.J." <biocjh at gmail.com>
> To: 3DEM Mailing List <3dem at ncmir.ucsd.edu>
> Subject: Re: [3dem] Virus on Carbon
> Message-ID:
> <CACVGmPBkve2fVL_9_N+_gk=30cd3QfBbBMjVgE+qRYXgBxORMA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> I also came accross problems of something like Luiza's. My sample is a
> macromolecule.
>
> Xinghong, whether your method could solve my problem? Thanks.
>
>
>
> 2014-03-14 12:16 GMT+08:00 Xinghong Dai <bestdz at gmail.com>:
>
>> Hi Luiza,
>>
>> Maybe you can try to make the ice a little bit thicker to see if that will
>> make any difference. They theory is that, if the ice is too thin, big
>> particles will not stay in the hole due to size exclusion effect. I had
>> similar situation when working with big viruses.
>>
>> Good luck!
>>
>>
>>
>> Xinghong
>>
>>
>>
>>
>>
>> *???**:* 3dem-bounces at ncmir.ucsd.edu [mailto:3dem-bounces at ncmir.ucsd.edu] *??
>> *Luiza Mendon?a
>> *????:* Thursday, March 13, 2014 4:41 PM
>> *???:* 3DEM Mailing List
>> *??:* [3dem] Virus on Carbon
>>
>>
>>
>> Dear colleagues,
>>
>>
>>
>> I work with HIV particles and (at least in my samples), they like the
>> carbon film on the grids much better than the holes, but for me this is a
>> big problem, as, even using high titer preps, they rarely go to the holes,
>> resulting in less-than-perfect tomograms. Has anyone else had this problem?
>> What did you do to solve it?
>>
>> My particles are resusspended in PBS (with gold fiducials) at the time of
>> freezing.
>>
>>
>>
>> Best,
>>
>> Luiza.
>>
>> _______________________________________________
>> 3dem mailing list
>> 3dem at ncmir.ucsd.edu
>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>>
>>
>
>
> --
> Regards!
> C.J.
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> ------------------------------
>
> Message: 3
> Date: Thu, 13 Mar 2014 21:30:42 -0700
> From: Xiaodong Yan <xyan at ucsd.edu>
> To: Wim Hagen <wim.hagen at embl.de>
> Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Subject: Re: [3dem] EMI to MRC image format conversion
> Message-ID: <7E5863EE-F319-4147-8940-543B2253C303 at ucsd.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Dear Wim,
>
> Thank you so much for the detailed information! What you said is exactly right. Currently, I am getting the ser files, so that it can be converted to mrc easily.
>
> Thanks a lot!
>
> Xiaodong
>
>
> On Mar 13, 2014, at 5:20 PM, Wim Hagen <wim.hagen at embl.de> wrote:
>
>> Dear Xiaodong,
>>
>> The only way to get stuck with EMI images is by collecting data manually with TIA software. TIA has an option to batch-convert a folder of EMI files to TIF.
>> As mentioned by others there are many programs that will convert the accompanying SER files to MRC but this just leads to unnecessary data storage of double the data.
>>
>> Another option for future data collection could be to collect with SerialEM: you can still collect manually but can also add a bit of (semi) automation to e.g. minimize image drift, autofocus, take image and save it.
>> This will be saved in TIF or MRC format with all metadata possibly needed later in a text file. When you have a Falcon camera: it also supports frames with a nice setup dialog and the frames are saved in 16 bit MRC stacks instead of the seven 32 bit raw images from FEI.
>>
>> EMI file format was developed to store multiple detector data in ESvision from EMIspec (later acquired by FEI, currently http://appfive.com), one of the first programs many years ago that was able to integrate data collection and data storage of e.g. stem, eels and eds data from different detector hardware vendors in one file, stuff made for material scientists, quite revolutionary 20 years ago, but fairly useless for cryo-EM imaging nowadays where MRC seems to be preferred by many.
>>
>> Best,
>>
>> Wim Hagen
>> EMBL Heidelberg
>>
>>> On Mar 14, 2014, at 0:11, Xiaodong Yan <xyan at ucsd.edu> wrote:
>>>
>>> Dear Colleagues,
>>>
>>> does anybody know which program can convert FEI EMI format image to MRC format image?
>>>
>>> thank you very much!
>>>
>>> xiaodong
>>>
>>> --
>>> Xiaodong Yan, Ph.D.
>>> University of California, San Diego
>>> Department of Chemistry and Biochemistry
>>> 9500 Gilman Drive, NSB 4107, MC-0378
>>> La Jolla, CA, 92093-0378
>>> (858) 534-5852
>>>
>>> _______________________________________________
>>> 3dem mailing list
>>> 3dem at ncmir.ucsd.edu
>>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 13 Mar 2014 21:32:44 -0700
> From: Steven Ludtke <sludtke at bcm.edu>
> To: Victor K <kvic45 at gmail.com>
> Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Subject: Re: [3dem] EMI to MRC image format conversion
> Message-ID: <8C1503CC-A1E3-495A-AF2D-C24A1B520C1D at bcm.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> I will add that the conversion process for .ser (or any other format) is pretty painless in EMAN2:
>
> e2proc2d.py file.ser file.mrc
>
>
> ----------------------------------------------------------------------------
> Steven Ludtke, Ph.D.
> Professor, Dept. of Biochemistry and Mol. Biol. Those who do
> Co-Director National Center For Macromolecular Imaging ARE
> Baylor College of Medicine The converse
> sludtke at bcm.edu -or- stevel at alumni.caltech.edu also applies
> http://ncmi.bcm.edu/~stevel
>
>
>
> On Mar 13, 2014, at 4:34 PM, Victor K <kvic45 at gmail.com> wrote:
>
>> Hi Xiaodong,
>>
>> If you have accompanying .ser files, many programs now read them. Eman2 certainly can. EMI is a proprietary format and is not supposed to be used by us unworthy scientists.
>>
>> Cheers,
>> Victor
>>
>>
>> Dear Colleagues,
>>
>> does anybody know which program can convert FEI EMI format image to MRC format image?
>>
>> thank you very much!
>>
>> xiaodong
>>
>> --
>> Xiaodong Yan, Ph.D.
>> University of California, San Diego
>> Department of Chemistry and Biochemistry
>> 9500 Gilman Drive, NSB 4107, MC-0378
>> La Jolla, CA, 92093-0378
>> (858) 534-5852
>>
>> _______________________________________________
>> 3dem mailing list
>> 3dem at ncmir.ucsd.edu
>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>> _______________________________________________
>> 3dem mailing list
>> 3dem at ncmir.ucsd.edu
>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
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