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CELLPROFILER PYTHON SOFTWARE
CELLPROFILER PYTHON DOWNLOAD

Nonzero values evaluate to True, so the image is first rescaled to its supported maximum intensity and then rescaled again according to the provided value. This boolean rescale is not passed into the call to read. It's first scaled by supported maximum intensity (option 2 or 3) and then scaled again by the user specified value.

We won't be dependent on python-bioformats to load images and rescale values (this is very important for 3D work).

It won't rescale all values to be teeny-tiny if metadata is missing and the data type is 32-bit integer (in this case, all values would be rescaled by dividing by 65535.

It's consistent and not dependent on image metadata.

Rescaling intensities in this way has the following benefits: That is, rescale intensities between 0 and 1 such that the actual minimum intensity value is mapped to 0 and the actual maximum intensity value is mapped to 1 (and all other intensities are adjusted accordingly): image = (image - image.min())/(image.max() - image.min())

Instead of defaulting to rescaling by supported maximum intensity (options 2 or 3), CellProfiler should default to rescaling intensities by actual maximum intensity. The maximum value supported by the image data type**.The maximum intensity supported by the image, as defined in the image metadata.Let us know if you encounter a bug by submitting a GitHub issue.Ĭurrently, when loading an image, intensities are rescaled based on the following criteria:

CELLPROFILER PYTHON DOWNLOAD

You can download a beta release for macOS and Windows from the CellProfiler website. If you’re an enthusiastic CellProfiler user, you should try the beta release of CellProfiler. Let us know if we’ve inadvertently broken your module by submitting a GitHub issue. You can download a nightly release for macOS and Windows from the CellProfiler website. If you’re the maintainer of a third-party CellProfiler module, you should use the nightly release of CellProfiler. Instructions for compiling CellProfiler on Linux, macOS and Windows are available from CellProfiler’s GitHub wiki.

If you’re contributing or planning to contribute to CellProfiler, you should compile CellProfiler from source. You can download a stable release for macOS and Windows from the CellProfiler website. We recommend the stable release of CellProfiler. What version of CellProfiler should I use? More information can be found in the CellProfiler Wiki.

CELLPROFILER PYTHON SOFTWARE

CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.