Cryosparc tool - installation & usage

Scripting
1

Dear colleagues,

I want to import dmoc from SerialEM to a usable XML format.
(BTW. It is a good idea for future improvement for CS to be able to read mdoc as well)

So I found the following thread -
Import ImageShift from .mdoc files (SerialEM) - Scripting - CryoSPARC Discuss

For this I have to use cryosparc tool.

Installing the cryosparc tool from
Getting Started — cryosparc-tools

it is not well clear to me how to start using it.

Firstly, could you please prompt me on how I can run the cryosparc tool after installation?
Secondly, do I understand correctly that the topic here
Import ImageShift from .mdoc files (SerialEM) - Scripting - CryoSPARC Discuss

Is the method now updated, as well as the script needed to import ImageShift from .mdoc files (SerialEM)?
cs_jiffies/cs_mdoc_image_shift.py at main · ccgauvin94/cs_jiffies · GitHub

If so, could you please prompt on the correct usage of the last script with cryosparc tools?

Thank you.

Kind regards,
Dmitry

2

Assuming you installed cryosparc-tools into a python virtual environment and you have access to the relevant ports of your CryoSPARC instance, you could either

  • write a python script and, from inside the python virtual environment, run it like
    python /path/to/your_script.py
  • or also install inside your python virtual environment a python notebook application, like jupyterlab, then write and run a notebook.
  • or …
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