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janni [2019/07/09 14:46] twagner [Installation] |
janni [2020/09/28 16:29] 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 during training. This now happens when ' | ||
+ | * 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 |