Hugh Warden

Hi @ap--, This is the code I run: ``` from locale import normalize from tifffile import imread from csbdeep.utils import normalize from stardist.models import StarDist2D from shapely.geometry import Polygon from...

I ran the `python -m paquo config --search-tree` command and chose one of the directories. I then ran `python -m paquo config --list --default > /path/to/.paquo.toml` and changed > java_opts...

I am definitely running `python -m paquo config --list` in the same directory as I am running the code from. I changed the .paquo.toml putting in `-XX: MaxRAMPercentage=4`. This showed...

Thanks very much! Paquo is a really useful bit of kit that is giving me a lot more flexibility in my workflows. Please let me know if I can help...

 Example of rotationally variant feature. We have manually identified many translationally and rotationally variant features in the output of CellProfiler.

There's no way of calculating this on a dataset, but you can via experimentation. I have some python code that generates "synthetic" cells (just 2 channel jpg's) of an ellipse...

An example of the texture features being rotationally variant:  These features are rotationally variant but information can be salvaged as they are phased and essentially trade off with one...

I agree that defining biologically irrelevant features is a very dependent task. but the suggestion would be not to remove features that are biologically irrelevant but to remove features that...

(1) The code is back from when I was new to Python so it's messy but I've uploaded it here: https://github.com/hwarden162/synthetic-cells-proto. It models cells as various simple Polygons and then...

To add to this, here is an example of a "synthetic cytoplasm" that I generate for this.  I fill the shape with anistropic spatially correlated noise that can be...