callum-jpg
callum-jpg
The watershed analysis code has been split into 3 functions in `object_processing`: `watershed_distance`, `watershed_markers` and `watershed_advanced`. `watershed_advanced` will makes calls to both watershed_distance and watershed_markers before doing some additional processing....
A [user on the forum](https://forum.image.sc/t/bug-in-cellprofiler-modifies-image-when-measuring-granularity/74057) has reported that the `MeasureGranularity` module erroneously alters the input_image. Any module downstream of `MeasureGranularity` has therefore been working with an altered image. This is...
The beginnings of adding threshold to CellProfiler library has raised some questions. Currently, the only functions added to cellprofiler.library.functions.image_processing are `get_threshold_robust_background` and `get_threshold`. `get_threshold` is used within the Threshold module...
When using CellProfiler in the GUI, pixel intensities are by default rescaled between [0, 1]. However, as a portion CellProfiler's functionality is moved into the discrete cellprofiler.library, does it make...
From: https://forum.image.sc/t/cell-profiler-issue-metadata-retrieval-and-running-a-pipeline-without-crashing/63861/2 If a user imports a multichannel image file, eg. tif, and uses the metadata module to extract metadata from image file headers and then presses the update button,...
With increasing support for 3D image analysis, it would be great to also have a 3D viewer within CellProfiler beyond just plane exploration. This viewer could provide side-profile views at...
Outstanding todo: - [ ] Add object processing functionality to `functions.object_processing` so that `cellprofiler.library.modules` is essentially just an API for `functions`. (This is implemented in principle for IDPrimary in the...
MeasureImageOverlap needs sklearn
Decisions/questions that need to be addressed before merge: - Input objects are expected to be in the dense format, but is this the best choice? - I chose dense since...