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tbepler / topaz

Pipeline for particle picking in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Also featuring micrograph and tomogram denoising with DNNs.
GNU General Public License v3.0
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Input micrographs as file #47

Closed rfleiro closed 3 weeks ago

rfleiro commented 4 years ago

Hi guys, great software :)

It would be great if topaz could take a file with a list of micrographs as input

Is this a possibility at all right now?

tbepler commented 4 years ago

At which stage? Topaz train accepts micrographs listed in an image list file. For downstream steps that expect micrographs to be listed on the command line (i.e. topaz extract), bash can do this for you using $(cat file.txt). For example,

topaz extract $(cat micrograph_list_file.txt)

will pass each line of "micrograph_list_file.txt" to topaz extract as a separate argument.

rfleiro commented 4 years ago

Thanks for the quick reply

I realise now I didn't specify. I was wondering if a list file could be provided for pre-process and denoising

I am indeed passing the input mics using a similar approach, thanks for the suggestion

tbepler commented 4 years ago

I'll add passing micrograph inputs through a file to the list for extra features to add in the future. If this is something you're interested in working on, I'd be happy to accept a pull request with this feature.

In the meantime, the bash approach above seems like the best way to deal with this.

tbepler commented 4 years ago

I added this in commit 752c140a709c745dabdcc2232b6e9444a11e1ef1