2D Stardist keeps crashing when Generating prediction(s) from unseen dataset

Open
#265 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
25/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
jupyter-notebook
Domain
cloud, machine-learning

Research direction

The issue names no file or test; start with the 2D Stardist prediction workflow and reproduce it in Colab using the reported 301-image, 16-bit stack while observing the failure and RAM usage. Done means predictions complete without requiring Colab Pro, with the reported dataset size covered by a regression check.

Written by the indexing model from the issue text.

Description

Describe the bug:

2D Stardist keeps crashing when Generating prediction(s) from unseen dataset. The unseen dataset is a stack of 301 images, each image is 16 bit and about 4MB.
Upon crashing, the suggestion is to upgrade to Colab pro to have more RAM.
Is there a solution to this, without having to upgrade and pay?

Desktop (please complete the following information):

  • OS: macOS Monterey 12.1
  • Browser: Safari
  • Version: 15.3

Thanks in advance,

Giuseppe

Dominant language
Jupyter Notebook
Stars
652
Forks
144
No merged PRs in 30d

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

More from HenriquesLab/ZeroCostDL4Mic

All issues in HenriquesLab/ZeroCostDL4Mic

Similar issues

More Cloud issues

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.