janni

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Just Another Noise 2 Noise Implementation (JANNI)

JANNI implements a neural network denoising tool described in NVIDIA's noise2noise paper: Noise2Noise: Learning Image Restoration without Clean Data - arXiv

It can be trained on your data without the need of ground truth images. It supports MRC and TIFF format.

JANNI can be used a command line tool but also provides an simple interface to integrate into other programs (see developer information).

This is an example where we applied JANNI:

The denoised micrographs are likely bad to use for further processing besides picking.

JANNI

Version: 0.1.0

Uploaded: 16. September 2019

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JANNI General Model

Version: 20190703 (Trained on 1xFalcon 2, 3x Falcon 3, 7xK2 datasets from Arctica / Krios)

Uploaded: 03. July 2019

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- Issue 0 (Version 0.0.1): On some machines (maybe related to ubuntu 16.04) JANNI complains that imagecodecs module (module for tiff files) cannot be found. However, imagecodecs-lite is installed and the error also occurs if you try to denoise MRC. pip uninstall imagecodecs-lite helps.

The following instructions assume that pip and anaconda or miniconda are available.

1. In case you have a old JANNI environment installed, you might want to remove the old one with:

conda env remove --name janni

2. After that, create a new virtual environment:

conda create -n janni -c anaconda python=3.6 cudnn=7.1.2 libtiff wxPython=4.0.4

3. Activate the environment:

source activate janni

Now can install JANNI either for GPUs or for CPUs:

4a. For GPU: Install JANNI form PyPi for a GPU machine:

pip install janni[gpu]

4b. For CPU: Install JANNI form PyPi for a CPU machine:

pip install janni[cpu]

You can cite JANNI using the Zenodo DOI:

DOI

JANNI 0.1.0

  • Add GUI
  • API changes for crYOLO 1.5

JANNI 0.0.5

  • Downgrade tensorflow and numpy again as it leads to long initialization times for some users.

JANNI 0.0.4

  • Improved selection of validation data
  • Add more data augmentation
  • Updated libraries (To Tensorflow 1.12.3 and numpy 1.15.4) to make it compatible with crYOLO
  • /web/sphire/www/sphire/wiki/data/pages/janni.txt
  • Last modified: 2019/10/14 14:54
  • by twagner