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GrotjahnLab / surface_morphometrics

Morphometrics for Membrane Surfaces Segmented from Cryo-ET or other volumetric imaging.
GNU General Public License v3.0
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Integration in Scipion tomo? #1

Open pconesa opened 2 years ago

pconesa commented 2 years ago

Hi! Congratulations for this work.

I was wondering if integrating this into the scipion tomo ecosystem is something you would like to do.

Scipion can:

Do the installation, in this case creating a conda environment. Smoothly integrate you software with the rest in the field.

Let me know, we can assist in the development process and codevelop the integration

pconesa commented 2 years ago

HI again, in case you were not aware of what scipion is:

Scipion site: http://scipion.i2pc.es/

We recently organized a course on tomography. Content is deposited here: Tutorials for tomography: https://scipion-em.github.io/docs/docs/user/user-documentation.html#tomography-tutorials

If you prefer videos, the course was recorded: https://www.youtube.com/watch?v=RNlmYUepqWc&list=PLyJiuGnB9hAx8uy1g_4F4ypfOqvQjyCqU

All the best

bbarad commented 2 years ago

So sorry for the delayed response - I've been underwater with other work the past few days. I'd be very very interested in integrating into scipion! I was super happy to see scipion integrate EMRinger (my first "polished" methods work), and I've been watching the pyseg integration with interest, and making our software more accessible (and making bookkeeping easier for users) would be a huge plus.

In terms of my immediate todo list, I want to:

  1. Set up a simplified conda.yml install file so that its a 1-step install. I assume this would also help with the scipion integration?
  2. Do some minor refactoring in the quantification code, which is currently a mix of general and reusable functions and mitochondria-specific routines that I'll need to get rid of before an integration is sensible.
  3. Write a detailed tutorial (ideally an interactive one!).

I think it might be appropriate to start talking about steps to integrate between 2. and 3. - do you agree?

pconesa commented 2 years ago

Great!

I completely agree . Having 1 done will simplify installation through scipion (optional but highly appreciated by our users) and probably easier to interact with. We can also assist if you need. We have large experience now packaging and installing stuff.

Let's do this, once you feel 1 is ready we talk again. Meanwhile, if we have time we can prepare a plugin skeleton.

El vie., 28 ene. 2022 18:22, Benjamin Barad @.***> escribió:

So sorry for the delayed response - I've been underwater with other work the past few days. I'd be very very interested in integrating into scipion! I was super happy to see scipion integrate EMRinger (my first "polished" methods work), and I've been watching the pyseg integration with interest, and making our software more accessible (and making bookkeeping easier for users) would be a huge plus.

In terms of my immediate todo list, I want to:

  1. Set up a simplified conda.yml install file so that its a 1-step install. I assume this would also help with the scipion integration?
  2. Do some minor refactoring in the quantification code, which is currently a mix of general and reusable functions and mitochondria-specific routines that I'll need to get rid of before an integration is sensible.
  3. Write a detailed tutorial (ideally an interactive one!).

I think it might be appropriate to start talking about steps to integrate between 2. and 3. - do you agree?

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bbarad commented 2 years ago

I've made my environment.yml file - ended up being way more of a pain than I expected due to conflicting dependencies in some of the packages! Reference commit: 48c1e5f0a89e3216ed791efc073c848b082dc456

pconesa commented 2 years ago

I'm sure you are making your users life easier with this change.

El sáb., 2 abr. 2022 18:27, Benjamin Barad @.***> escribió:

I've made my environment.yml file - ended up being way more of a pain than I expected due to conflicting dependencies in some of the packages! Reference commit: 48c1e5f https://github.com/GrotjahnLab/surface_morphometrics/commit/48c1e5f0a89e3216ed791efc073c848b082dc456

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bbarad commented 2 years ago

I've gotten v0.2 of the software out, with much more consistent pipelining for running the software. I think now may be a good time to come back around to scipion integration if you are still interested!

pconesa commented 2 years ago

Sure, what about scheduling a meeting to discuss how to proceed and update each other on the status?

bbarad commented 2 years ago

Sounds good - I am in GMT-7, so I am guessing morning meeting for me is the easiest overlap for you? I think any day but Wednesday next week would work for me!