Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Interested in contributing to Skopy? #2

Closed
0x00b1 opened this issue Aug 21, 2017 · 1 comment
Closed

Interested in contributing to Skopy? #2

0x00b1 opened this issue Aug 21, 2017 · 1 comment

Comments

@0x00b1
Copy link

0x00b1 commented Aug 21, 2017 •
edited
Loading

I have been working on a similar application Skopy. It can be used for feature extraction (i.e. similar to CellProfiler’s measurement modules), but I plan on adding image segmentation and object detection in the near future. It has nearly the same mission, providing a ready-made pipeline for image analysis, but it has a simple, portable, and lightweight architecture and people have already started using it. Would you be interested in contributing? It could be fun!
@freeman-lab
Copy link
Contributor

Hey @0x00b1! Thanks so much for sharing, we hadn't seen skopy, and it looks like a really cool effort. This package starfish is currently pretty focused on prototyping a standard pipeline for image-based transcriptomics analysis, as opposed to a more general image processing / feature extraction / pipeline tool -- consider this a learning exercise to get us started.

We're also super interested in working on or helping to improve those kinds of more general tools. As we start to go in that direction, we'll definitely dig into skopy -- as well as all the other tools in this ecosystem, of course! -- and hopefully we can find a way to collaborate.

@ttung ttung mentioned this issue May 28, 2019
Merged
ttung pushed a commit that referenced this issue May 31, 2019
RFC: clean up max projection
55edf6c 
1. Remove ImageStack.max_proj.  Steer users towards using Filter.MaxProject.
2. Move the core functionality of max_proj to _max_proj() as it is used commonly in internal code.
3. Refactor ISS notebook to use Filter.MaxProject.

#2 is somewhat debatable.  I feel there is a good case that all internal code that wants to run max_projection should already have been reduced.

Test plan: travis
ttung pushed a commit that referenced this issue Jun 21, 2019
RFC: clean up max projection
ea9ae4d 
1. Remove ImageStack.max_proj.  Steer users towards using Filter.MaxProject.
2. Move the core functionality of max_proj to _max_proj() as it is used commonly in internal code.
3. Refactor ISS notebook to use Filter.MaxProject.

#2 is somewhat debatable.  I feel there is a good case that all internal code that wants to run max_projection should already have been reduced.

Test plan: travis
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@0x00b1 @dganguli @freeman-lab