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====== Just Another Noise 2 Noise Implementation (JANNI) ====== | ====== Just Another Noise 2 Noise Implementation (JANNI) ====== | ||
- | JANNI implements a neural network denoising tool described in NVIDIA' | + | JANNI implements a neural network denoising tool described in NVIDIA' |
- | [[https:// | + | |
It can be trained on your data without the need of ground truth images. It supports MRC and TIFF format. | 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 [[janni_tutorial# | + | JANNI can be used a command line tool but also provides an simple interface to integrate into other programs (see [[:janni_tutorial# |
- | < | + | |
* **License**: | * **License**: | ||
- | * **GitHub repository**: | + | * **GitHub repository**: |
- | </ | + | </ |
- | This is an example where we applied JANNI: | + | |
- | {{ :: | + | {{ : |
+ | |||
+ | <note important> | ||
- | <note important> | ||
- | The denoised micrographs are likely bad to use for further processing besides picking. | ||
- | </ | ||
==== Download ==== | ==== Download ==== | ||
+ | |||
=== JANNI === | === JANNI === | ||
- | Version: 0.2 | ||
- | Uploaded: | + | Version: 0.3.1 |
+ | |||
+ | Uploaded: | ||
[[https:// | [[https:// | ||
=== JANNI General Model === | === JANNI General Model === | ||
+ | |||
Version: 20190703 (Trained on 1xFalcon 2, 3x Falcon 3, 7xK2 datasets from Arctica / Krios) | Version: 20190703 (Trained on 1xFalcon 2, 3x Falcon 3, 7xK2 datasets from Arctica / Krios) | ||
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[[https:// | [[https:// | ||
+ | |||
==== Known Issues ==== | ==== Known Issues ==== | ||
+ | |||
- < | - < | ||
==== Installation ==== | ==== Installation ==== | ||
- | 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: | + | 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 | conda env remove --name janni | ||
+ | |||
</ | </ | ||
- | 2. After that, create a new virtual environment: | + | 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 | + | conda create -n janni -c conda-forge |
</ | </ | ||
- | 3. Activate the environment: | + | 3. Activate the environment: |
< | < | ||
source activate janni | source activate janni | ||
+ | |||
</ | </ | ||
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< | < | ||
pip install janni[gpu] | pip install janni[gpu] | ||
+ | |||
</ | </ | ||
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< | < | ||
pip install janni[cpu] | pip install janni[cpu] | ||
+ | |||
</ | </ | ||
+ | |||
==== Getting started ==== | ==== Getting started ==== | ||
- | [[janni_tutorial|Here you can find a tutorial how to denoise your micrograghs | + | |
+ | [[:janni_tutorial|Here you can find a tutorial how to denoise your micrographs | ||
==== How to cite ==== | ==== How to cite ==== | ||
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You can cite JANNI using the Zenodo DOI: | You can cite JANNI using the Zenodo DOI: | ||
- | < | + | < |
- | <a href=" | + | |
- | </ | + | |
==== Changelog ==== | ==== Changelog ==== | ||
- | **JANNI 0.1.2** | + | |
- | * Added support for binning. In case you recorded your movies in super resolution | + | **JANNI 0.3.1:** |
- | mode, but later want to apply JANNI to binned images, you need to bin your images | + | |
- | during training. This now happens when ' | + | * Fix dependency issue with protobuf (Thanks to Tapu Shaikh) |
- | the super resolution movies. The file ' | + | |
- | * JANNI now allows to choose between two loss functions: mean squared error (mse) or mean absolute | + | **JANNI 0.3:** |
- | error (mae). The latter is the new default. | + | |
+ | * Update dependencies and fix setup. | ||
+ | |||
+ | **JANNI 0.2.2:** | ||
+ | |||
+ | * Fix an issue that JANNI can't denoise a single image (it only worked for folders) (Thanks to Sony Malhotra) | ||
+ | |||
+ | **JANNI 0.2.1:** | ||
+ | |||
+ | * Because of an libary update, JANNI was not working anymore (No supported model) (Thanks to | ||
+ | |||
+ | Sony Malhotra) . | ||
+ | |||
+ | **JANNI 0.2** | ||
+ | |||
+ | | ||
+ | * JANNI now allows to choose between two loss functions: mean squared error (mse) or mean absolute error (mae). The latter is the new default. | ||
**JANNI 0.1.2** | **JANNI 0.1.2** | ||
+ | |||
* Fix installation procedure. | * Fix installation procedure. | ||
**JANNI 0.1.0** | **JANNI 0.1.0** | ||
+ | |||
* Add GUI | * Add GUI | ||
* API changes for crYOLO 1.5 | * API changes for crYOLO 1.5 | ||
**JANNI 0.0.5** | **JANNI 0.0.5** | ||
+ | |||
* Downgrade tensorflow and numpy again as it leads to long initialization times for some users. | * Downgrade tensorflow and numpy again as it leads to long initialization times for some users. | ||
- | * | + | * |
**JANNI 0.0.4** | **JANNI 0.0.4** | ||
+ | |||
* Improved selection of validation data | * Improved selection of validation data | ||
* Add more data augmentation | * Add more data augmentation | ||
* Updated libraries (To Tensorflow 1.12.3 and numpy 1.15.4) to make it compatible with crYOLO | * Updated libraries (To Tensorflow 1.12.3 and numpy 1.15.4) to make it compatible with crYOLO | ||
+ | |||
+ |