Microscoper is a simple wrapper for python-bioformats, with added features, such as saving images based on the filters used while acquiring them (For example: DAPI.tif for a Z stack of images acquired using the DAPI channel).
To install microscoper with pip
pip install microscoper
Or install the latest development version from github:
git clone https://github.com/pskeshu/microscoper.git
cd microscoper
pip install -e .
Navigate to any folder which has microscope images in bioformats supported format, and in the terminal run the following command:
microscoper -f . -k .vsi
The -f path/to/images flag specifies the directory in which to look for files that have the keyword specified by -k .vsi. By default, -f looks into all directories under the specified directory. So, if you have a directory structure like this:
|-cells
|---control
|-----image_1.vsi
|-----image_2.vsi
|-----40X
|-------image_3.vsi
|---treatment
|-----image_1.vsi
|-----image_2.vsi
If you input microscoper -f cells/, all the images in the subdirectories will be taken as the input. Note that the -k argument is optional if you're working with .vsi files, as it takes -k .vsi by default.
The defaults for -f is . or the current directory. If the working directory is /home/user/data/exp/cells for the directory tree given above, running microscoper alone is sufficient.
In case you want to make sure the right files are being converted, you can initiate a dry run by passing an addition --list argument. For the above directory tree, the dry run will return something like this:
$ pwd
/home/user/data/exp/cells
$ microscoper --list
./control/40X/image_3.vsi
./control/image_1.vsi
./control/image_2.vsi
./treatment/image_1.vsi
./treatment/image_2.vsi
======================
Total files found: 5
======================
Dry run will exit without converting the supported files to TIFF.
This program has only been tested with Olympus CellSense format, .vsi, but can potentially be used with any bioformats supported file format. Supply the file format with the -k argument.
If you want microscoper to work with your favourite proprietary image format, send me a sample image.
- Input files pattern matching with wildcards and regular expressions.
- Write meta data to text files, or directly to the TIFF files.
Feel free to fork this repository to modify the program as you seem fit, or submit push requests.