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janni [2019/07/09 14:46] twagner [Installation] |
janni [2020/09/28 16:27] twagner [Changelog] |
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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: | This is an example where we applied JANNI: | ||
{{ :: | {{ :: | ||
+ | |||
+ | <note important> | ||
+ | The denoised micrographs are likely bad to use for further processing besides picking. | ||
+ | </ | ||
==== Download ==== | ==== Download ==== | ||
=== JANNI === | === JANNI === | ||
- | Version: 0.0.4 | + | Version: 0.2 |
- | Uploaded: | + | Uploaded: |
[[https:// | [[https:// | ||
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Uploaded: 03. July 2019 | Uploaded: 03. July 2019 | ||
- | [[https:// | + | [[https:// |
==== Known Issues ==== | ==== Known Issues ==== | ||
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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 | + | conda create -n janni -c anaconda python=3.6 cudnn=7.1.2 libtiff |
</ | </ | ||
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</ | </ | ||
- | Now can install JANNI either for GPUs or for CPUs: | + | Now can install JANNI either for GPUs **or** for CPUs: |
- | **For GPU:** | + | 4a. **For GPU:** Install JANNI form PyPi for a GPU machine: |
- | 4. Install JANNI form PyPi for a GPU machine: | + | |
< | < | ||
pip install janni[gpu] | pip install janni[gpu] | ||
</ | </ | ||
- | **For CPU:** | + | 4b. **For CPU:** Install JANNI form PyPi for a CPU machine: |
- | 4. Install JANNI form PyPi for a CPU machine: | + | |
< | < | ||
pip install janni[cpu] | pip install janni[cpu] | ||
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==== Getting started ==== | ==== Getting started ==== | ||
- | [[janni_tutorial|Here you can find a tutorial how to denoise your microgragh | + | [[janni_tutorial|Here you can find a tutorial how to denoise your micrograghs |
+ | |||
+ | ==== How to cite ==== | ||
+ | |||
+ | You can cite JANNI using the Zenodo DOI: | ||
+ | |||
+ | < | ||
+ | <a href=" | ||
+ | </ | ||
+ | |||
+ | |||
+ | ==== Changelog ==== | ||
+ | **JANNI 0.2** | ||
+ | * Added support for binning. In case you recorded your movies in super resolution | ||
+ | mode, but later want to apply JANNI to binned images, you need to bin your images | ||
+ | | ||
+ | the super resolution movies. The file ' | ||
+ | * 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** | ||
+ | * Fix installation procedure. | ||
+ | |||
+ | **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 |