Adding email chain:
Well we could do this but it is really an ugly hack to fix a bug in the template picking program caused by not taking rectangular images into account properly. It would be better to fix the actual bug.
In the meantime one thing you could do is to:
1. Pick using templates.
2. make a stack that will exclude the edged.
3. Convert the stack to picks again. Use these for the Relion etc. run.
This is also a hack but one that does not require any programming.
Best regards,
Bridget
One possible solution would be to include a "border threshold" to exclude particles that are picked at X pixels of the border of the micrograph. That would bypass the problem.
After/during particle picking but before particle extraction.
I could suggest that to Neil if you like.
Thanks,
Yacob
From: Gomez, Yacob
Good afternoon Bridget,
Thanks for taking your time to email me and taking care of this.
Let me explain how I see it:
They way I work is:
first, I treat the data with Appion after the data collection.
That is the easiest, fastest and most useful thing to do after collecting data with Leginon.
It allows me to process and analyze data on the fly, and adjust my data collection based on the results. Also little by little I am learning to use more features of the suite.
For several reasons I decide to switch from Appion to other EM programs after particle picking. You know most of them:
1. Appion allows particle picking based on templates, and that is something that is interesting for my projects.
2. But unfortunately, for later steps of the image processing, like 2D classification and all the following steps, the CPU usage is big and the users are not allowed to run those jobs on the computing resources of the NYSBC, at least not with a reasonable number of cores/job.
3. Install a package like Appion, which also wraps many other EM programs is complicated in an external institution cluster. But I am trying.
4. There is no feature that allows to remove automatically particles from the carbon with enough accuracy. I have to do it manually. So I use EMAN.
5. Relion is my first choice for data processing. I am familiar with the package, with its original suite (Xmipp) and the developer. Besides, it gives excellent results.
6. Relion likes to do its own gray-scale normalization, so particles must be extracted with Relion, as recommended by the developer.
Therefore, for my own preferences, but also for practical reasons (specially reasons 4 and 6), my possibilities are either pick the particles in Appion or not to do it, but the particle extraction must be performed by Relion.
At least it is strongly recommended by the developer in order to have the best results. Correct me if I am wrong.
So I read the answer from Neil, but I didn't consider that option because the reasons that I am explaining.
Thank you!
Yacob
From: Bridget Carragher [bcarr@nysbc.org]
Hi Yacob,
As you see various people are thinking about this. It is likely some issue of assuming that images are square - as indeed the always used to be! Anyway as Neil mentioned, this bug should not affect you as the stack maker should automatically ignore any parties that close to an edge of the image. Let us know if you want to discuss more.
Best regards,
Bridget
