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pr4deepr / GutAnalysisToolbox

Analysis and characterisation of cells within the gut wall using deep learning models. The current focus is on studying enteric neurons and enteric glia.
https://gut-analysis-toolbox.gitbook.io/docs/
BSD 3-Clause "New" or "Revised" License
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Use rescale factor instead of pixel size #8

Closed pr4deepr closed 2 years ago

pr4deepr commented 2 years ago

Currently the user selects the pixel size to rescale the images, so the cells to be segmented have the same size as the images used for training the model. This increases the accuracy of the segmentation. Using the term pixel size can be confusing. Instead, we should use the term rescaling factor. Rescaling factor can be calculated by dividing the pixel size of the users image by 0.568 or whatever pixel size of the images the model has been trained on.

pr4deepr commented 2 years ago

Perhaps rename pixel size to rescale factor instead of changing the whole code?

pr4deepr commented 2 years ago

Added in: https://github.com/pr4deepr/GutAnalysisToolbox/commit/4a0b887df7b86d1ae5731827b37bc2c1b6f3cc11