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Running notebooks locally
guijacquemet edited this page Dec 1, 2021
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In order to run ZeroCostDL4Mic notebooks locally, it is important to ensure that the correct packages are installed. We recommend creating a new Conda environment on your local machine for every notebook that you intend to use and installing the required packages with pip from a requirements file.
For instance, to create a Conda environment to run the 3D U-Net notebook locally follow these steps:
- Open a notebook in Google Colab from the wiki page and import the required packages
- Download
requirements.txt
from the Files tab located in the upper left corner of the Google Colab notebook
- To create a new Conda environment on your local machine, run
$ conda create -n myzerocostenv python=3.6.9
in the terminal - Next, activate your new environment by running
$ conda activate myzerocostenv
- To install the necessary packages navigate to the location of
requirements.txt
and run$ pip install -r requirements.txt
- Let us know if you encounter any issues and enjoy ;)
These tutorials were written by Seyed Hosseini and funded by Abo Akademi University's "Open Science" initiative.
Video tutorial | Text-based tutorial |
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(coming soon)
Main:
- Home
- Step by step "How to" guide
- How to contribute
- Tips, tricks and FAQs
- Data augmentation
- Quality control
- Running notebooks locally
- Running notebooks on FloydHub
- BioImage Modell Zoo user guide
- ZeroCostDL4Mic over time
Fully supported networks:
- U-Net
- StarDist
- Noise2Void
- CARE
- Label free prediction (fnet)
- Object Detection (YOLOv2)
- pix2pix
- CycleGAN
- Deep-STORM
Beta notebooks
Other resources: