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From: Dmitry S. <sem...@gm...> - 2017-02-16 10:34:23
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Dear colleagues, When you use *xmipp3 - optical alignment* what values you are using for the GPU? Is there also an option to run that process using the Threads/MPI? And do you *enable* *Use previous movie alignment t*o SUM frames option if you* run** protocol* upon * xmipp3 - correlation alignment?* Sincerely, Dmitry |
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From: Carlos O. S. <co...@cn...> - 2017-02-15 22:15:49
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Dear Dmitry, On 02/15/17 14:04, Dmitry Semchonok wrote: > Dear colleagues, > > I have a question about *xmipp3 - correlation alignment.* > > In Advanced option if I change to > > *Filter at* 2.5 A (instead of 4) This filter is used to downsample the images resulting in a speed-up and removal of noise (just for the record, the alignment operation is performed at a sampling rate of newTs=0.9*maxFreq/2, meaning that this maximum frequency is mapped to the digital frequency 0.45, Nyquist is at 0.5). Remind that this program is simply looking for a shift between every pair of frames, and then combining all that information in a single shift per frame. In this sense, I would doubt that very high frequencies result in a significant change of the shift (the spectrum up to 4A should be informative enough to be able to detect 2 numbers, X and Y shift). > > *Maximum shift (pixels) *from 30 to 50 The maxShift is used to search in the autocorrelation function for the maximum cross correlation peak between -maxShift to +maxShift. This is the maxShift between any two pairs of frames. If you expect larger shifts, then you may certainly increase this value. If you don't expect these large shifts, then by increasing the maxShift parameter you are increasing the probability of identifying a spurious correlation due to noise as the largest correlation peak, resulting in an incorrect estimate of the shift between the two frames (still, the algorithm combining all shifts between pairs in a shift for the frame explicitly looks for outliers, so that you noisy identification still may be harmless). I hope I had clarified how the algorithm works, Carlos Oscar > > Will the script work more accurate and precise? > > Thank you! > > Sincerely, > Dmitry > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://biocomp.cnb.csic.es National Center of Biotechnology (CSIC) c/Darwin, 3 Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ------------------------------------------------------------------------ |
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From: Josue Gomez-B. <su...@bc...> - 2017-02-15 14:20:18
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Hi Dmitry Semchonok,
I think that the left half image is the PSD before alignment, but maybe I can be wrong. Could you send an image that you believe is inverted? Please, send too the movie and tell us the protocol used and the parameters to reproduce the protocol.
THanks
Activo Mie, 15 Febrero at 2:20 PM
, Dmitry Semchonok <sem...@gm...> Escrito:
Dear colleagues,
Again considering xmipp3 - correlation alignment script.
In SCIPION version 1.1 (yet developer I suppose) the
Compare PSD before/after seems to be reversed (first goes after and then before)
Correct me if I'm wrong
Sincerely,
Dmitry
|
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From: Josue Gomez-B. <su...@bc...> - 2017-02-15 14:10:45
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Hi Dmitry Semchonok,
Maybe is a good exercise to learn all of us, if you try execute the correlation with your suggested parameters, and share your results. Carlos Oscar, who is the person that implemented this method and the person in charge of Xmipp, can clarify you this parameters.
Activo Mie, 15 Febrero at 2:04 PM
, Dmitry Semchonok <sem...@gm...> Escrito:
Dear colleagues,
I have a question about xmipp3 - correlation alignment.
In Advanced option if I change to
Filter at 2.5 A (instead of 4)
Maximum shift (pixels) from 30 to 50
Will the script work more accurate and precise?
Thank you!
Sincerely,
Dmitry
|
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From: Pablo C. <su...@bc...> - 2017-02-15 13:53:34
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Dear Dmitry,
Scipion should be consistent and offer you MPI/Threads and GPU if make sense.
Please, go and try whatever Scipion GPU protocols for offer. If you find any incompatibilities, let us know.
All the best, Pablo.
Activo Mie, 15 Febrero at 12:12 PM
, Biocomputing unit - National Center for Biotechnology <sc...@cn...> Escrito:
Hi Dmitry, Not all of them are in GPU.
Those that are in GPU are:
motioncorr, motioncor2, gautomatch, relion 2, gctf, and igbmc-auto-picking.
As a general rule, those that run with GPU have some GPU related parameter like "GPU ID:".
It might be nice to identify them more clearly.
All the best, Pablo
Activo Mie, 15 Febrero at 11:42 AM
, Dmitry Semchonok <sem...@gm...> Escrito:
Dear colleagues,
I would like to know if I can run all protocols in the SCIPION using the GPU?
If not then which one I currently can?
Is it only motioncor?
What about relion 2-3D?
Sincerely,
Dmitry
|
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From: Dmitry S. <sem...@gm...> - 2017-02-15 13:20:46
|
Dear colleagues, Again considering *xmipp3 - correlation alignment *script. In SCIPION version 1.1 (yet developer I suppose) the Compare PSD before/after seems to be reversed (first goes after and then before) Correct me if I'm wrong Sincerely, Dmitry |
|
From: Dmitry S. <sem...@gm...> - 2017-02-15 13:04:36
|
Dear colleagues, I have a question about *xmipp3 - correlation alignment.* In Advanced option if I change to *Filter at* 2.5 A (instead of 4) *Maximum shift (pixels) *from 30 to 50 Will the script work more accurate and precise? Thank you! Sincerely, Dmitry |
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From: Dmitry S. <sem...@gm...> - 2017-02-15 12:28:18
|
Dear colleagues, Thank you for the answer about the protocols that currently supports GPU usage. Which protocol can use *more than one GPU*, or which ones can combine one or more *GPUs and MPI/threading*? For example, Motioncor2 does seem to support multiple GPUs, but it does not say anything about MPI: http://msg.ucsf.edu/em/software/motioncor2.html Sincerely, Dmitry |
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From: Pablo C. <su...@bc...> - 2017-02-15 11:12:47
|
Hi Dmitry, Not all of them are in GPU.
Those that are in GPU are:
motioncorr, motioncor2, gautomatch, relion 2, gctf, and igbmc-auto-picking.
As a general rule, those that run with GPU have some GPU related parameter like "GPU ID:".
It might be nice to identify them more clearly.
All the best, Pablo
Activo Mie, 15 Febrero at 11:42 AM
, Dmitry Semchonok <sem...@gm...> Escrito:
Dear colleagues,
I would like to know if I can run all protocols in the SCIPION using the GPU?
If not then which one I currently can?
Is it only motioncor?
What about relion 2-3D?
Sincerely,
Dmitry
|
|
From: Dmitry S. <sem...@gm...> - 2017-02-15 10:42:37
|
Dear colleagues, I would like to know if I can run all protocols in the SCIPION using the GPU? If not then which one I currently can? Is it only motioncor? What about relion 2-3D? Sincerely, Dmitry |
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From: Jose M. de la R. T. <del...@gm...> - 2017-02-15 00:16:28
|
Hi Juha, There is a special monitor called "summary monitor". You need to provide as input the all preceding protocols and the monitor will be giving you in one shot: 1) how many items have been processed so far in each steps 2) CTF defocus values plot 3) an HTML report that you can easily monitor from a web-browser. Hope this helps, Jose Miguel On Tue, Feb 14, 2017 at 11:25 PM, Juha Huiskonen <ju...@st...> wrote: > Hello all, > > I am running Scipion (a recent devel branch) in streaming mode for the > first time. I am importing movies, run MotionCor2, followed by CTFFIND4 / > GCTF and this is working really nicely. > > What is currently the best way to collate outputs from these in a report > form? I saw some references to HTML reports on github... > > Best wishes, > Juha > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Juha H. <ju...@st...> - 2017-02-14 22:26:31
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Hello all, I am running Scipion (a recent devel branch) in streaming mode for the first time. I am importing movies, run MotionCor2, followed by CTFFIND4 / GCTF and this is working really nicely. What is currently the best way to collate outputs from these in a report form? I saw some references to HTML reports on github... Best wishes, Juha |
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From: Jose M. de la R. T. <del...@gm...> - 2017-02-13 11:32:17
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Dear Dmitry, Thanks for giving a try to Scipion devel. Nonetheless, I would suggest you to use 'release-1.1' branch (recently branched out from devel) which is the branch for the next stable release. This means that it will only contains important bug-fixes and should be more stable than devel at this point. Regarding your specific questions, in this new version we have separated the protocols related to movie alignment. Before, they were added to the same protocol...was does not follows the Scipion philosophy of modularity. This change was also necessary for the streaming feature, that allows you to launch several processing steps right after the first item of the set is being produced and does not need to wait until all items are done. This allows to overlap the acquisition time with the preprocessing time, that save computing time and resources while giving you a quickly feedback on the dataset. Probably you are not seeing these new protocols because you still have an old 'protocols.conf' file. Try to delete this file (at $SCIPION/config/protocols.conf) and then generate it again with the command: scipion config After that you should have the complete list of movie alignment protocols (see the attached screenshot) under the Movies section in the left panel of the project GUI. Hope this helps Jose Miguel [image: Inline image 1] On Sat, Feb 11, 2017 at 8:26 PM, Dmitry Semchonok <sem...@gm...> wrote: > Dear colleagues, > > I tried SCIPION dev - wanted to experiment with GPU etc. > And found some workflow differences. > > > I used to do the motion correction with *xmipp3 movie alignment* based on > motion core (cross-corr + optical correction using CPU) > > > Now I can only see: > > *xmipp3 - optical alignment*; (this is probably local?) > *grigoriefflab - unblur* > *grigoriefflab - summovie* > > > So, how do you do motion alignment (global and local) now after adding > your movie to the project? Can I use GPU? > > And after how to sum the movies? (grigoriefflab - ?) > > Sincerely, > Dmitry > > > > > > > > > > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Dmitry S. <sem...@gm...> - 2017-02-11 19:26:54
|
Dear colleagues, I tried SCIPION dev - wanted to experiment with GPU etc. And found some workflow differences. I used to do the motion correction with *xmipp3 movie alignment* based on motion core (cross-corr + optical correction using CPU) Now I can only see: *xmipp3 - optical alignment*; (this is probably local?) *grigoriefflab - unblur* *grigoriefflab - summovie* So, how do you do motion alignment (global and local) now after adding your movie to the project? Can I use GPU? And after how to sum the movies? (grigoriefflab - ?) Sincerely, Dmitry |
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From: Carlos O. S. <co...@cn...> - 2017-02-10 19:50:44
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Dear Dmitry, On 02/08/17 12:09, Dmitry Semchonok wrote: > Dear colleagues, > > 1. > I have a problem with the data - the pixel size of 1 data set is > different form the 2nd one. > > Does anyone know how to *change the pixel size* of a *movie stack > before* adding it to the project? Any software? At this moment, you cannot change the pixel size at the level of movie stack, but you can when extracting the particles. At that point you can make both datasets to have exactly the same pixel size. > > (I know that on the particles level we can use *xmipp - crop/resize > particle* script but I rather want to avoid that) > > The idea is to combine 2 data sets in 1 folder (after pixel > equalization) and then > add it to the SCIPION project. If you do it from the command line, you may try xmipp_image_resize -i inputMovie.mrcs -o outputMovie.mrcs --factor 1.02 where the factor 1.02 is the ratio between the two sampling rates. > > 2. > About the CTF binning. > > Let say you binned your CTF estimation to 2. > Is the 2ce binned CTF estimation is more reliable and still describes > the higher frequencies? > Or no binning is preferable? No binning should be preferred, as long as the Thon rings are sufficiently visible so that the estimation can be reliably performed, for instance, if the Thon rings are too concentrated at the origin, then the estimation may go wrong. Cheers, Carlos Oscar > > > thank you. > > > Sincerely, > Dmitry > > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://biocomp.cnb.csic.es National Center of Biotechnology (CSIC) c/Darwin, 3 Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ------------------------------------------------------------------------ |
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From: Sheng Li <bi...@gm...> - 2017-02-10 01:04:35
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Dear All,
I kept receiving such error. could anyone please take a look and give some
advices?
Scipion v1.0.0 (2016-02-20) Augusto
>>>>> python
/home/public/Downloads/scipion/pyworkflow/apps/pw_protocol_run.py
"/home/public/ScipionUserData/projects/TestMixedBPV2"
"Runs/000301_XmippProtCropResizeParticles/logs/run.db" "301"
Run ML2D
** Running command: 'python /home/public/Downloads/scipion/scipion
runprotocol pw_protocol_run.py
"/home/public/ScipionUserData/projects/TestMixedBPV2"
"Runs/000355_XmippProtML2D/logs/run.db" 355'
Scipion v1.0.0 (2016-02-20) Augusto
>>>>> python
/home/public/Downloads/scipion/pyworkflow/apps/pw_protocol_run.py
"/home/public/ScipionUserData/projects/TestMixedBPV2"
"Runs/000355_XmippProtML2D/logs/run.db" "355"
>>> ERROR running protocol scipion - ml2d
FAILED with error:
[ FAILED ] TestMixedBPV2.test_workflow
Traceback (most recent call last):
File
"/home/public/Downloads/scipion/software/lib/python2.7/unittest/case.py",
line 329, in run
testMethod()
File
"/home/public/Downloads/scipion/pyworkflow/tests/em/workflows/test_workflow_mixed.py",
line 170, in test_workflow
self.launchProtocol(protML2D)
File "/home/public/Downloads/scipion/pyworkflow/tests/tests.py", line 83,
in launchProtocol
raise Exception("ERROR launching protocol.")
Exception: ERROR launching protocol.
|
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From: Carlos O. S. <co...@cn...> - 2017-02-09 07:58:40
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Dear Dmitry, On 07/02/2017 11:40, Dmitry Semchonok wrote: > Dear colleagues, > > could you please explain me the strategy of binning usage? > > Apart of the fact that binning speeds up the processing. I would like > to use the binning to see my particles better (some of my data is very > close to focus) Binning, or better downsampling (the difference is in the filter used before the decimation of the signal) is not only used for speeding up the processes, but also to remove high frequency noise, and smoothing the objective function of many algorithms. Actually, binning is not the best option as it has negative effects in many subsequent steps (see http://biocomp.cnb.csic.es/~coss/Articulos/Sorzano2009d.pdf) > > In the SCIPION tutorial - Mix-and-Match Tutorial > <https://github.com/biocompwebs/scipion/wiki/tutorials/scipion_tutorial_betagal.pdf> > on the page 12 stands the *Preprocess particles protocol *that sugests > to do binning before CTF estimation. > > My questions are: > > 1. When do you do unbinning of the dataset? The set is never unbinned, you can extract particles again at the original size and reuse the part of the processing that you did with the downsampled particles. > > 2. Do you also need to estimate the CTF for the unbinned dataset? No. Actually, the best way is to estimate the CTF on the original micrographs and use the same CTF for all particles (regardless their downsampling). Scipion knows the sampling rate of the particles and the sampling rate at which the CTF was estimated and acts accordingly. > > 3. How / when do you do the binning if you work with movies (stucks) - > after the motion correction? > Again, better do the movie alignment before extracting at a downsampled size. > > > > Another issue: > > there is a new soft calling cryoSPARC > > see the link about cryoSPARC > <http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4169.html?WT.feed_name=subjects_systems-biology> > > > Do you have plans to incorporate it in the SCIPION? > > We have contacted the authors of cryoSparc and we will see how far we can go from both sides. Kind regards, Carlos Oscar > Sincerely, > Dmitry > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://biocomp.cnb.csic.es National Center of Biotechnology (CSIC) c/Darwin, 3 Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ------------------------------------------------------------------------ |
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From: Pablo C. <pc...@cn...> - 2017-02-08 13:12:30
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Dear Dmitry, For the question (1.) is it possible to arrange a remote desktop sharing session to see what's going on? For 2, yes, Scipion will take care of "interpolating" the coordinates (on binned micrographs) to original micrographs. On 02/02/17 15:19, Dmitry Semchonok wrote: > Dear colleagues, > > 1. Wienner filter + CTF envelope correction --> relion 2D error > (normalisation). > > I did the CTF correction of the particle using Wiener filter script + > correct for the CTF envelope I had a problem running the corrected > particles in relion 2D alignment (in the settings of relion I selected “NO” > for the CTF correction). > > The error: > > Error: it appears that these images have not been normalized to an average > background value of 0 and a stddev value of 1 > > Then I tried relion - preprocessing tool > Outcome: finished but in the log: > WARNING! Stddev on image …… > Xmipp_ProtCTFCorrectedWiener2D/corrected_ctf_particles.stk is zero! > Skipping normalisation > > Tried Xmipp - preprocessing tool > Outcome - finished no error. > > But again - when you run relion 2D alignment you getting the same error. > > Why? > > > 2. Particle picking. > > Probably very basic question but it is still not a routine for me. > > Now I’m collecting the data on Titan Krios and one of the outcome is the > binned jpg file where you can see your particles nicely. > Do we have the similar tool in the SCIPION that will allow us to initially > bin the images, pick the particles and then interpolate the coordinates on > unbinned images? > (Normally I don't really use the binning). > > Is that what we can do using the CTF estimation script? > If so how and when can/should we unbin the dataset? > > > Sincerely, > Dmitry > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Dmitry S. <sem...@gm...> - 2017-02-08 11:09:17
|
Dear colleagues, 1. I have a problem with the data - the pixel size of 1 data set is different form the 2nd one. Does anyone know how to *change the pixel size* of a *movie stack before* adding it to the project? Any software? (I know that on the particles level we can use *xmipp - crop/resize particle* script but I rather want to avoid that) The idea is to combine 2 data sets in 1 folder (after pixel equalization) and then add it to the SCIPION project. 2. About the CTF binning. Let say you binned your CTF estimation to 2. Is the 2ce binned CTF estimation is more reliable and still describes the higher frequencies? Or no binning is preferable? thank you. Sincerely, Dmitry |
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From: Jose M. de la R. T. <del...@gm...> - 2017-02-07 17:22:12
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Dear Dennis, In Scipion is is easy to move project between computers. A project is just a folder inside $SCIPION_USER_DATA/projects/ So, you only need to make sure that there is not running any protocol and you can just copy that folder. Something that break when moving the project is the path of the initial import files, but usually are micrographs or movies and they are not needed for continuing some steps of the processing. I do not understand the issue related to updating the workflow chart...could you specify more the current situation? Kind regards, Jose Miguel On Tue, Feb 7, 2017 at 5:57 PM, Dennis Thomas < dt...@pr...> wrote: > Dear list > > I began working on a 12 processor local linux box and want to move the > project to a larger cluster to continue refinement. Can I just copy the > project folders to the disks on the new cluster or is better to start a new > project and import particles for example. > > Also the workflow chart quit updating after CTF correction. Hitting > refresh or closing or reopening doesn't change this any ideas. The results > are there so I keep moving along. But it does make it difficult to > visualize results also. > > thanks, > > Dennis > > -- > Dr. Dennis Thomas > Cryo-EM Facility Manager > Center for Integrative Proteomics Research > Rutgers University > Phone: 848-445-5302 > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Dennis T. <dt...@pr...> - 2017-02-07 17:13:45
|
Dear list I began working on a 12 processor local linux box and want to move the project to a larger cluster to continue refinement. Can I just copy the project folders to the disks on the new cluster or is better to start a new project and import particles for example. Also the workflow chart quit updating after CTF correction. Hitting refresh or closing or reopening doesn't change this any ideas. The results are there so I keep moving along. But it does make it difficult to visualize results also. thanks, Dennis -- Dr. Dennis Thomas Cryo-EM Facility Manager Center for Integrative Proteomics Research Rutgers University Phone: 848-445-5302 |
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From: Jose M. de la R. T. <del...@gm...> - 2017-02-07 10:59:55
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Dear Luigi, As Pablo mentioned before, there are just a few particles per micrograph. This means that, for using Xmipp picker, you need to manually pick in several micrographs, train in other and then go for the automatic one. I also tried with Eman2 boxer and I couldn't get it to pick properly in the micrographs that you sent me, but I'm not an Eman expert. Regarding the Ethan picker, I added the protocol after Juha request, but it is still in a development branch named 'ethan-pick'. I hope Juha could give you more information about how to use it. Kind regards, Jose Miguel. On Feb 6, 2017 8:57 AM, "Luigi De Colibus" <lu...@st...> wrote: Dear Pablo and Jose Miguel, Thank you for your email. In the past I used to run the automatic particle picking in ETHAN on my data and it always worked even if I had few particles per micrographs. Unfortunately the current version of SCIPION that I’m running doesn’t contain ETHAN and that’s why I tried to use Xmipp and Boxer with no success. I also tried to run ETHAN outside SCIPION and subsequently import the particles coordinates in SCIPION but it didn’t work. SCIPION was complaining about the file format, which was an EMAN1 format. However, one of my colleague (Juha Huiskonen ) told me that now it’s possible to update SCIPION to the version which includes ETAHAN too; so I will ask to our system manager to update our version of SCIPION and hopefully all my problems will be fixed. Cheers Luigi Luigi De Colibus,PhD University of Oxford Wellcome Trust Centre for Human Genetics Division of Structural Biology Roosevelt Drive Oxford OX3 7BN ---- Original message ---- >Date: Fri, 3 Feb 2017 19:11:25 +0100 >From: Pablo Conesa <pc...@cn...> >Subject: Re: [scipion-users] About particle picking with Xmipp and EMAN2 through Scipion >To: lu...@st...,Jose Miguel de la Rosa Trevin < del...@gm...> > >Hi Luigi! I can see that there are at most, 4 viruses per micrograph. > > >Xmipp picking needs at least 15 (in one micrograph) in order to train it >and learn. I might be wrong, sure Jose Miguel can correct me. > >As for the Eman, I can't make it autopick, but might be that I have few >viruses, I'll contact a some colleagues (on monday must be) that might >help with this. > >Have a nice weekend, Pablo > >Scipion team. > > >On 03/02/17 18:21, Luigi De Colibus wrote: >> Dear Pablo and Jose Miguel, >> >> I'm just wondering if you have received my previous email through my Gmail account with attached micrographs. >> >> Thanks >> >> Luigi >> >> >> Luigi De Colibus,PhD >> University of Oxford >> Wellcome Trust Centre for Human Genetics >> Division of Structural Biology >> Roosevelt Drive >> Oxford OX3 7BN >> >> >> ---- Original message ---- >>> Date: Fri, 3 Feb 2017 11:39:17 +0100 >>> From: Pablo Conesa <pc...@cn...> >>> Subject: Re: [scipion-users] About particle picking with Xmipp and EMAN2 through Scipion >>> To: Jose Miguel de la Rosa Trevin <del...@gm...>,lui gi...@st...,sci...@li... >>> >>> Dear Luigi, please follow this thread. Jose Miguel, >>> I already replied to Luigi, and asked for the same >>> thing. Let's keep this thread since situation is >>> better explained. >>> >>> Cheers, Pablo >>> >>> Scipion Team >>> >>> On 03/02/17 11:32, Jose Miguel de la Rosa Trevin >>> wrote: >>> >>> Dear Luigi, >>> >>> Thanks for providing feedback to us. Regarding >>> your specific issues with picking, what do you >>> mean by "after providing the references" in Xmipp >>> and Eman pickers? To the best of my knowledge, >>> both programs generate the references on-the-fly, >>> after the selection of some particles manually. >>> So, there is not need to provide pre-computed >>> references such as 2D class averages. >>> >>> In the case of EMAN2-Box, both the >>> manual/supervised steps are interwinned in a very >>> interactive way. On the other hand, in Xmipp3 >>> picker, those steps are separated in two phases. >>> You first need to picking manually some >>> micrographs entirely (or a well-defined box in one >>> micrograph is its contains many particles)...and >>> then switch to "Supervised" mode, where the >>> algorithm will propose you some particle >>> candidates and you can correct it (either removing >>> bad proposed particles or adding missing one). The >>> algorithm will "learn" from that and then in >>> another protocol you can launch the automatic >>> picking based on that training. >>> >>> Anyway, if you provide a few micrographs we could >>> try to help about the parameters selection. >>> >>> Hope this helps, >>> >>> Jose Miguel >>> >>> Scipion Team >>> >>> ----------------------------------------- >>> >>> My name is Luigi De Colibus and I’m Post >>> Doc at the Division of Structural Biology of >>> Oxford University. >>> I’m writing you because I’m trying >>> to run automated particle picking programs on my >>> micrographs trough SCIPION. >>> Surprisingly, despite the fact my virus particle >>> is very big and evident on the micrographs, >>> neither Xmipp particle picking program nor Boxer >>> in EMAN2 is able to pick correctly the particles >>> after providing the reference. >>> I guess my settings could be wrong and trying >>> different values has not helped so far. >>> >>> It would be great if you could point me in the >>> right direction. >>> I can send you one of my micrographs if you need >>> to do a test run. >>> >>> Thanks a lot in advance for your help! >>> >>> Best Regards >>> >>> Reply to: luigi at strubi.ox.ac.uk >>> >>> ------------------------------------------------------------ ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Dmitry S. <sem...@gm...> - 2017-02-07 10:40:35
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Dear colleagues, could you please explain me the strategy of binning usage? Apart of the fact that binning speeds up the processing. I would like to use the binning to see my particles better (some of my data is very close to focus) In the SCIPION tutorial - Mix-and-Match Tutorial <https://github.com/biocompwebs/scipion/wiki/tutorials/scipion_tutorial_betagal.pdf> on the page 12 stands the *Preprocess particles protocol *that sugests to do binning before CTF estimation. My questions are: 1. When do you do unbinning of the dataset? 2. Do you also need to estimate the CTF for the unbinned dataset? 3. How / when do you do the binning if you work with movies (stucks) - after the motion correction? Another issue: there is a new soft calling cryoSPARC see the link about cryoSPARC <http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4169.html?WT.feed_name=subjects_systems-biology> Do you have plans to incorporate it in the SCIPION? Sincerely, Dmitry |
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From: Dmitry S. <sem...@gm...> - 2017-02-06 10:49:23
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Dear colleagues, I would like to try the developer version of the SCIPION. Could you please forward me to the downloading page? Is that an idea to add these info on the main download page as that was with XMIPP? Sincerely, Dmitry |
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From: luigi De C. <lui...@gm...> - 2017-02-03 11:54:09
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Dear Pablo and Jose Miguel, Thank you very much for your replay. I’m sorry if I didn’t make myself clear in my previous email. By "after providing the references" I meant that I picked manually few particles and then I saved them, subsequently I tried to use them as reference in the automatic particle picking programs but it didn’t work; essentially the boxes were not overlapped on the particles. I also played with the settings but didn’t make any difference. Attached you will find a couple of my micrographs to do test run. Best Regards Luigi Nov22_03.55.56_SumCorr.mrc.gz <https://drive.google.com/file/d/0B4-b-9va8rKEcFJkRG1hMWJ2QW8/view?usp=drive_web> Nov22_04.01.08_SumCorr.mrc.gz <https://drive.google.com/file/d/0B4-b-9va8rKEODloYVZyUHFVSEk/view?usp=drive_web> Nov22_03.57.24_SumCorr.mrc.gz <https://drive.google.com/file/d/0B4-b-9va8rKEZU5oVVVsOWRFRXM/view?usp=drive_web> |
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