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.

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

Improving classification performance. #301

Open
adamltyson opened this issue Apr 26, 2021 · 0 comments
Open

Improving classification performance. #301

adamltyson opened this issue Apr 26, 2021 · 0 comments
Labels
cellfinder-core Issue concerns the core backend enhancement New feature or request help wanted Extra attention is needed

Comments

@adamltyson
Copy link
Member

General issue to track ideas for how to improve classification performance. Possible areas to investigate include:

Easier

  • Look at effects of batch size on processing time. Can we set the most appropriate batch size based on computing resources available?
  • Look at effects of multiprocessing. Is there a generally optimal number of workers?
  • Improve batch generation. The cube generator does not always return "full" batches (i.e. if there is only one cell candidate in a plane, that batch will only have one set of cuboids).
  • Caching - the generator doesn't cache any data, so once planes 0-19 are loaded, the next set of batches will reload 1-20.

More difficult

  • How accurate can we get without the background channel?
  • Investigate the network itself:
    • What is the optimal network depth?
    • Can the network be trained in a more optimal way?
    • Can we use another, more efficient network architecture?

cc @satyakam7

@adamltyson adamltyson added enhancement New feature or request help wanted Extra attention is needed labels Apr 26, 2021
@adamltyson adamltyson self-assigned this Apr 26, 2021
@adamltyson adamltyson removed their assignment Feb 14, 2022
willGraham01 referenced this issue in brainglobe/cellfinder-core Aug 24, 2023
* remember parameters

* fix FOV

* fix FOV processing

* Bump version: 0.0.3-rc2 → 0.0.3-rc3

* Bump version: 0.0.3-rc3 → 0.0.3

* fix bug adding training data layers

* fix bug when exporting saved training data

* Bump version: 0.0.3 → 0.0.4-rc0

* run detection in thread worker

* Add info to header

* reset params

* Fix for #2 implemented

* match training plugin to detection

* only import cellfinder when starting plugins

* extract cubes in thread

* train in separate thread

* Update readme
@willGraham01 willGraham01 added the cellfinder-core Issue concerns the core backend label Jan 3, 2024
@willGraham01 willGraham01 transferred this issue from brainglobe/cellfinder-core Jan 3, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
cellfinder-core Issue concerns the core backend enhancement New feature or request help wanted Extra attention is needed
Projects
Status: Backlog
Development

No branches or pull requests

2 participants