Demonstrate image download process and prepare for full image download for JUMP plate BR00117006 #36
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jenna-tomkinson
approved these changes
Oct 25, 2024
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| # quality of life for jupyter environments | ||
| # ---------------------------------------- | ||
| # automatically converts .ipynb to .py file on save within jupyter lab | ||
| - conda-forge::jupytext | ||
| # dependency of jupyterlab_code_formatter | ||
| - conda-forge::black | ||
| # dependency of jupyterlab_code_formatter | ||
| - conda-forge::isort | ||
| # used for formatting code within .ipynb files | ||
| - conda-forge::jupyterlab_code_formatter |
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I really like this formatting here!
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Thanks @jenna-tomkinson ! After making a small change based on your notes in #35 to avoid redownloading images, I will now merge this in. |
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This PR demonstrates how we can download images from S3 paths using processed CytoTable data by referencing paths which originate from CellProfiler exports. For now, this work downloads images for the first row of data from BR00117006. That said, it is prepared to download the full image dataset with a small amount of changes. I'm queuing up this PR to make sure the work is reviewed prior to downloading the full dataset to conserve time.
I've also made adjustments to use Jupyter Lab through the project environment. Alongside this change I added two tools: JupyText (which automatically converts .ipynb files to .py files on notebook save), and jupyterlab_code_formatter (which automatically formats code as you write it within notebooks using Black and isort). These changes were added to help increase notebook development velocity.
Closes #31
Prepares for #32