README.md 1.12 KB
Newer Older
Christoph Sommer's avatar
Christoph Sommer committed
1
# convert_ometiff
Christoph Sommer's avatar
Christoph Sommer committed
2
Convert multi-file OME-Tiff files produced at Open-SPIM microscope to ImageJ hyper-stacks. Note, the pixel-size information is lost
Christoph Sommer's avatar
Christoph Sommer committed
3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18

## Installation
---

1. Recommended: download and install Python 3.6 using the Anaconda python distribution 
   from https://www.anaconda.com/download/. Anaconda already comes with 
   most of the required packages.
2. Download convert_ometiff and/or extract the convert_ometiff package to path/to/dir
3. Open (Anaconda) prompt and type 
```
cd path/to/dir
```
4. Install additional requirements
```
pip install -r requirements.txt
```
Christoph Sommer's avatar
Christoph Sommer committed
19 20 21 22
(Windows) If installing tifffile fails, download the tifffile .whl package from https://www.lfd.uci.edu/~gohlke/pythonlibs/ and install it with
```
pip install <tifffile-..-.whl>
```
Christoph Sommer's avatar
Christoph Sommer committed
23
5. Install the convert_ometiff package
Christoph Sommer's avatar
Christoph Sommer committed
24 25 26 27 28 29 30
```
python setup.py install
```
6. Quick test
```
convert_ometiff --help
```
Christoph Sommer's avatar
Christoph Sommer committed
31
If all went fine, the command line help is displayed.
Christoph Sommer's avatar
Christoph Sommer committed
32

Christoph Sommer's avatar
Christoph Sommer committed
33 34 35 36 37
## Usage

Open (Anaconda prompt)
```
convert_ometiff <dir/containint/ometiffs> [<dir/containing/ometiffs>]
Christoph Sommer's avatar
Christoph Sommer committed
38 39 40 41 42
```

## Planned updates
1. Include meta-data such as pixel-sizes
2. More flexible pattern matching