https://github.com/brisvag/fidder

Detect and erase gold fiducials in cryo-EM images

https://github.com/brisvag/fidder

Repository

Detect and erase gold fiducials in cryo-EM images

https://github.com/brisvag/fidder/blob/main/

# fidder

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*fidder* is a Python package for detecting and erasing gold fiducials in cryo-EM
images.


    


Fiducials are detected using a pre-trained residual 2D U-Net at 8 /px. Segmented regions are replaced with white 
noise matching the local mean and global standard deviation of the image.

The package can be used from both
[Python](usage/python.md)
and the
[command line](usage/command_line.md).

---

## Quickstart

### Python

```python
import mrcfile
import torch
from fidder.predict import predict_fiducial_mask
from fidder.erase import erase_masked_region

# load your image
image = torch.tensor(mrcfile.read('my_image_file.mrc'))

# use a pretrained model to predict a mask
mask, probabilities = predict_fiducial_mask(
    image, pixel_spacing=1.35, probability_threshold=0.5
)

# erase fiducials
erased_image = erase_masked_region(image=image, mask=mask)
```
### Command Line

```bash
# predict fiducial mask
fidder predict \
--input-image example.mrc \
--probability-threshold 0.5 \
--output-mask mask.mrc

# erase masked region
fidder erase \
--input-image example.mrc \
--input-mask mask.mrc \
--output-image erased.mrc

```

---

## Installation

pip:

```shell
pip install fidder
```

### Compatibility

If trying to use an `10.X` CUDA runtime you may have to install older versions of 
`torch` and `pytorch-lightning`, see 
[teamtomo/fidder#17](https://github.com/teamtomo/fidder/issues/17) for details.

## Notes

This package provides similar functionality to 
[BoxNet](http://www.warpem.com/warp/?page_id=135) from Warp
when 
[retrained for gold fiducial segmentation](http://www.warpem.com/warp/?page_id=137).

This package was developed to make this functionality available in a standalone, 
easy to install Python package. The architecture and training data 
preprocessing are based on the description in the 
[Warp paper](https://doi.org/10.1038/s41592-019-0580-y).

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