Beth CiminiAdventures in… building Dockers for x86 on an M1Fun fact of the day — if you want to build non-ARM Dockers on an M1, the secret is to change your docker build commands to docker buildx…Jan 23, 2023Jan 23, 2023
Beth CiminiAdventures in… qualitative analysis file blindingOften in image analysis, if you want to confirm to yourself you’re seeing what you think you are seeing (especially if your phenotype is…Oct 13, 2022Oct 13, 2022
Beth CiminiAdventures in… debugging memory issues with Docker.VERY IMPORTANT PRO TIP — apparently, even running memory checks inside of a Docker (using vmstat -a -SM 1 1 ), the memory checks do not…Sep 20, 2022Sep 20, 2022
Beth CiminiAdventures in… numpy and pandas data replacement(I know there exists pandas/numpy documentation on this but I never look up the right function and I never find things structured the way I…Sep 16, 2022Sep 16, 2022
Beth CiminiAdventures in… running parallel. A lot.Say you hypothetically started some long-running scripts with GNU parallel, and you had enough jobs that they weren’t all going to run at…Sep 16, 2022Sep 16, 2022
Beth CiminiAdventures in… pandas with integer column headingsToday in ‘Beth’s random pandas tips’ — if your workflow involves iteratively saving then reading a CSV, don’t use ints as column names…Aug 23, 2022Aug 23, 2022
Beth CiminiAdventures in… extracting parts of a tarballStep 1 — make an AWS machine for this project with a hard drive that’s at minimum big enough for your tarball and the data itself that you…Aug 23, 2022Aug 23, 2022
Beth CiminiAdventures in Image Analysis EngineeringI often find myself making “mini-tutorial” threads in Slack for folks on my team about problems I run into and how they can solve them…Aug 23, 2022Aug 23, 2022