PythonForAivia

PythonForAivia copied to clipboard

Bumps [numpy](https://github.com/numpy/numpy) from 1.19.5 to 1.22.0. Release notes Sourced from numpy's releases. v1.22.0 NumPy 1.22.0 Release Notes NumPy 1.22.0 is a big release featuring the work of 153 contributors spread...

dependabot[bot]

Bumps [tensorflow-gpu](https://github.com/tensorflow/tensorflow) from 2.6.0 to 2.9.3. Release notes Sourced from tensorflow-gpu's releases. TensorFlow 2.9.3 Release 2.9.3 This release introduces several vulnerability fixes: Fixes an overflow in tf.keras.losses.poisson (CVE-2022-41887) Fixes a...

dependabot[bot]

Bumps [protobuf](https://github.com/protocolbuffers/protobuf) from 3.19.1 to 3.19.5. Release notes Sourced from protobuf's releases. Protocol Buffers v3.19.5 C++ Reduce memory consumption of MessageSet parsing This release addresses a Security Advisory for C++...

dependabot[bot]

https://github.com/AiviaCommunity/PythonForAivia/tree/master/VenvRecipes/CellposeVenv For this to happen, cellpose should choose to use a 2D or 3D recipe based on the input dimensions This allows Aivia to take advantage of Cellpose's novel separation...

tlancon

For example, see [here](https://stackoverflow.com/questions/60147430/display-multiple-frames-from-a-dcm-image-using-python-pydicom). For an example dataset I fixed the SamplesPerPixel tag, but it was still missing other tags. This could mean that for incorrectly saved DICOM images, there...

tlancon

2D+T not loaded back into Aivia correctly

1

Need to specify axes using imsave Example with skimage: skimage.io.imsave(resultLocation, outputData, None, {'axes':'XYZ'}) Example with tifffile: tifffile.imsave(f"{outpath}/my_TZCYX_data.tif", data, metadata={'axes': 'TZCYX'}) Do we need to say which axes are present for...

tlancon

Allows segmenting across multiple Z with superpixels

tlancon

Test using tifffile directly for imread/imsave

2

Allows more control over handling metadata and can fix issue with 2D+T

tlancon

Add API documentation to README

1

May need to branch this into its own file at some point, but for now we need to translate the example from the devs into the README

tlancon

The Aivia log is insightful, but mostly hidden from users. Make a section in README to show how to most rapidly develop and debug Python recipes by passing back/forth between...

tlancon