Commit 70cd4499 authored by Christoph Sommer's avatar Christoph Sommer

Update README.md

parent 92b5e472
......@@ -58,7 +58,12 @@ The installation of the CUDA toolkit is straight-forward. To download cuDNN you
2. NVidia CUDA toolkit 10.0 + cuDNN 7.5.1 + tensorflow 13.1 (recommended)
### Python dependencies
We strongly recommend using the [Anaconda Python distribution](https://www.anaconda.com/distribution/) with Python == 3.6. Furthermore, we recommend to create a new conda virtual environment with `conda create -n py36_bif_care python=3.6 anaconda`.
We strongly recommend using the [Anaconda Python distribution](https://www.anaconda.com/distribution/) with Python == 3.6. Furthermore, we recommend to create a new conda virtual environment for Python 3.6 with:
```
conda create -n py36_bif_care python=3.6 anaconda
conda activate py36_bif_care
```
You can install all mayor dependencies, including tensforflow (1.12.1) and csbdepp (0.3.0) by:
......@@ -66,6 +71,7 @@ You can install all mayor dependencies, including tensforflow (1.12.1) and csbde
cd <this-path>
pip install -r requirements.txt -e .
```
If you observe problems installing javabridge see troubleshooting below.
If your Python distribution comes without PyQt5, install it by:
......@@ -74,7 +80,7 @@ conda install pyqt
```
### IPython widgets
The user interface is written using IPython/Jupyter widgets, which requires the installation of [node.js]([nodejs](https://nodejs.org/en/))
The user interface is written using IPython/Jupyter widgets, which requires the installation of [node.js](https://nodejs.org/en/))
Finally, you have to install jypyter widgets and enable them, by:
......@@ -99,7 +105,7 @@ Unzip, copy and rename (e. g. *_low.tif*, *_high.tif*) the images form `low` and
* To install bioformats/ javabridge you need the Microsoft Visual Studio compiler runtime 2015 (14.0) installed, which is included with Microsoft Visual Studio community edition >=2017
* To install bioformats/ javabridge you need Java SDK 8 (1.8) or download [pre-compiled .whl](https://www.lfd.uci.edu/~gohlke/pythonlibs/) packages and install them by:
`pip install <javabridge>.whl` and `pip install <bioformats>.whl`
```pip install <javabridge_cp36_amd64>.whl` and `pip install <bioformatse_cp36_amd64>.whl```
......
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