Stitch images to form a montage.
Java development kit
Python 2.7.12
pip
- numpy
- $ pip install numpy
- scipy
- $ pip install scipy
- click
- $ pip install click
- skimage
- $ pip install skimage
- python-bioformats
- $ pip install python-bioformats
- matplotlib
- $ pip install matplotlib
Additional in Windows OS: Visual C++ 9.0
$ git clone https://github.com/CellProfiler/stitching.git
$ cd /path/to/stitching
$ pip install -e .
Users may notice that when opening and zooming the images in IDEAS (and also in ImageJ, IrfanView) the images appear to be higher resolution, but this is because the software has an adjustable DPI setting, which uses interpolation to scale the images up (adding pixels) for display and publication.
$ python stitching -o path/to/OUTPUT_DIRECTORY path/to/IMAGE
Generates per-channel tiled images from IMAGE saved to OUTPUT_DIRECTORY. Each image in IMAGE has shape 55px by 55px and is padded with random noise. Files are named "ch1.tif", "ch2.tif", ..., one for each channel.
Optional:
| --image-size | Set the window size of the tile images (default: --image-size 55). If user sets a size bigger than the original images, each of the tile images will be padded with its own background. If user sets a size smaller than the original images, each of the tile images will be cropped toward its center. |
| --montage-size | Set the size of the final montage (default: --montage-size 30). If the total number of original images could not fill up the desired montage size, the montage will be padded with black background.
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