empanada-napari#

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Getting Started

Step-by-step installation instructions for the latest version for new or returning users

Getting Started

Modules

Detailed descriptions of parameters, outputs and demo videos of all the modules included in empanada-napari

Modules

Tutorials

Indepth tutorials on how to finetune, train and run inference through this plugin

Tutorials

Share your model

Share your trained model with the us and the vEM community

Share your model

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Important

empanada-napari version 1.2 has new models for nuclei and lipid droplets, new plugins and updated 2D and 3D inference modules. Check out how to update to the latest version here!

Note

Windows users who are working with GPUs, please see an important note about installation steps in our FAQ section.

Suggested Workflow#

Suggested workflow diagram for empanada-napari

Citing this work#

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If you use results generated by this plugin in a publication, please cite:

Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model

Conrad, R., & Narayan, K.

(2023). Cell Systems, 14(1), 58-71. e5. //doi.org/10.1016/J.CELS.2022.12.006

https://www.cell.com/cell-systems/fulltext/S2405-4712(22)00494-X

This version of empanada-napari was created by Abhishek Bhardwaj https://cmm.ccr.cancer.gov/volume-em/