angelolab / angelolab/Nimbus-Inference

Product backlog

Abierto
#1 0 comentarios 0 reacciones 0 asignados Ver en GitHub
enhancement
Lenguaje dominante
Python
Estrellas
45
Forks
9
Métricas de merge de PR
Sin PR fusionados en 30 d

Descripción

### Description of feature

## Nimbus inference repo
- [x] Convert weights from tf to torch with [ivy](https://github.com/unifyai/ivy)
- [x] #27

## Nimbus inference class
- [x] Adapt from class from [Nimbus repo](https://github.com/angelolab/Nimbus/blob/main/src/cell_classification/inference.py)
- [x] Add tile & stitch inference
- [x] Add different data source structures (i.e. ome-tiff directories)
- [x] Add inference notebook comparable to [this one](https://github.com/angelolab/Nimbus/blob/main/templates/1_Nimbus_Predict.ipynb)
- [ ] Add easy-to-use and hackable commandline interface
- [x] Change user input half-resolution to the actual magnification level of the images and fix type casting mentioned in #26.

## Viewer Widget
- [x] Add viewer widget from [here](https://github.com/angelolab/Nimbus/blob/main/src/cell_classification/viewer_widget.py)
- [x] Make viewer widget work with less than three channels
- [x] Build a second viewer widget with channels on the left, instance map on the right and all cells gray except the one we're interested in in white.
- [x] Adapt the viewer to show marker images and gold-standard groundtruth next to each other

## General project
- [x] Make the data available (EMBL)
- [x] Clean up plot notebooks
- [x] Update the documentation and the pypi distribution

Guía de contribución

No hay ninguna guía de contribución indexada para este repositorio

Evaluación

Este issue todavía no se ha evaluado.

Recibe los nuevos issues en tu correo

Un resumen breve de issues de GitHub para principiantes.