arXiv
Abstract: The analysis of dynamic organelles remains a formidable challenge, though key to understanding biological processes. We introduce Nellie, an automated and unbiased pipeline for segmentation, tracking, and feature extraction of diverse intracellular structures. Nellie adapts to image metadata, eliminating user input. Nellie’s preprocessing pipeline enhances structural contrast on multiple intracellular scales allowing for robust hierarchical segmentation of sub-organellar regions. Internal motion capture markers are generated and tracked via a radius-adaptive pattern matching scheme, and used as guides for sub-voxel flow interpolation. Nellie extracts a plethora of features at multiple hierarchical levels for deep and customizable analysis. Nellie features a Napari-based GUI that allows for code-free operation and visualization, while its modular open-source codebase invites customization by experienced users.
Nellie's pipeline and Napari plugin are both very much in early stages, therefore I highly encourage any and all feedback.
https://github.com/aelefebv/nellie/assets/26515909/1df8bf1b-7116-4d19-b5fb-9658f744675b
Notes:
If not already installed, install Napari: https://napari.org/stable/tutorials/fundamentals/installation
Plugins > Install/Uninstall Plugins...
Install
pip install nellie
To use GPU acceleration via NVIDIA GPUs, you also need to install cupy:
pip install cupy-cudaXXx
cupy-cudaXXx
with the appropriate version for your CUDA version.
cupy-cuda11x
for CUDA 11.x or cupy-cuda12x
for CUDA 12.xThe sample dataset shown below is in the repo if you want to play around without, and can be downloaded here.
https://github.com/aelefebv/nellie/assets/26515909/05199fed-ed8c-4237-b3ba-0a3f4cdcb337
https://github.com/aelefebv/nellie/assets/26515909/372d07a8-15a0-4926-8594-108dd4b97280
napari
Plugins > Nellie (nellie)
then to the File select
tab.Select File
of Select Folder
to select your image(s).
Open preview
button once the metadata is filled in to ensure it looks correct.Process
tab.
Remove image edges
checkbox.Run Nellie
, or run individual steps below.
Visualization
tab can only be opened once its respective step has been run.[image_directory]/nellie_output/
.
Analyze
tab.
Visualization
tabRaw
: Visualize the raw data for the processed channel.Preprocessed
: Visualize the contrast-enhanced data.Segmentation
: Visualize the organelle and branch instance segmentation masks.Mocap Markers
: Visualize the mocap markers used for waypoints.Reassigned Labels
: Visualize the organelle and branch instance segmentation masks where voxels are reassigned based on the first timepoint.Alt+Click
on a label to visualize the track of that selected organelle/branch across all timepoints.
Toggle 2D/3D view
at the bottom left before Alt+Click
ing (eventually I'll get it to work while in 3D mode).https://github.com/aelefebv/nellie/assets/26515909/7f4f09a4-3687-4635-988d-e1d16ad2a4af
Analyze
tab, select the hierarchy level you want to visualize from the dropdown.Save graph
button. A .png will be saved to [image_directory]/nellie_output/graphs/
with the current datetime.Export graph data
button. A .csv will be saved to [image_directory]/nellie_output/graphs/
with the current datetime.Log scale
checkbox.Median view
checkbox.Overlay mask
button to colormap the organelle mask based on your selected feature.
Timepoint data
checkbox to allow you to select a specific timepoint to visualize via the slider.Easy screenshot
feature:
Easy screenshot
or hit Ctrl/Cmd-Shift-E after clicking your image.[image_directory]/nellie_output/screenshots/
with the current datetime.A few options are available for providing feedback or getting help with Nellie:
Github Issues | email | X | wherever else you can find me!
To avoid any unnecessary back-and-forth, please include any/all (if possible) of the following information in your bug report:
Nellie has been tested on the following configurations:
Nellie © 2024 by Austin E. Y. T. Lefebvre is licensed under CC BY 4.0
If you used Nelly or found this work useful in your own research, please cite our arXiv preprint:
Lefebvre, A. E. Y. T., Sturm, G., et. al. Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy, arXiv, 2024, https://arxiv.org/abs/2403.13214
@misc{lefebvre2024nellie,
title={Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy},
author={Austin E. Y. T. Lefebvre and Gabriel Sturm and Ting-Yu Lin and Emily Stoops and Magdalena Preciado Lopez and Benjamin Kaufmann-Malaga and Kayley Hake},
year={2024},
eprint={2403.13214},
archivePrefix={arXiv},
primaryClass={cs.CV}
}
https://github.com/aelefebv/nellie/assets/26515909/88578dc9-f5c5-4188-a0e2-4e37037a44a9
https://github.com/aelefebv/nellie/assets/26515909/db76d388-a9cc-4650-b93d-69d357ace418
https://github.com/aelefebv/nellie/assets/26515909/58bda3cb-6489-4620-8584-a3728cd6b2ec