From 586aa33011481134d1bc6c8bc211a69db2d08e90 Mon Sep 17 00:00:00 2001 From: Ilakkiyan Jeyakumar Date: Fri, 12 Apr 2024 16:14:53 -0700 Subject: [PATCH] Update README.md --- lfm_data_utilities/thumbnail_labelling/README.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/lfm_data_utilities/thumbnail_labelling/README.md b/lfm_data_utilities/thumbnail_labelling/README.md index b67fa598..2f61a20d 100644 --- a/lfm_data_utilities/thumbnail_labelling/README.md +++ b/lfm_data_utilities/thumbnail_labelling/README.md @@ -1,5 +1,11 @@ # Thumbnail Labelling +## Before you begin +Make sure you have already created a folder of images for the runs you are interested in. You can create a folder of images from a `.zarr` file by using `lfm_data_utilities/malaria_labelling/process_zarr_to_images.py`. An example usage would be: +`python3 process_zarr_to_images.py /hpc/projects/group.bioengineering/LFM_scope/ec50/drug_no_drug_comparison/2024-04-12-141644_`. + +Note that you need to pass in the _folder containing_ the zarr file and not the path to the zarr file itself. + ## Labelling Guide Given datasets (i.e. folder of images + folder of labels), grab a thumbnail of each cell and put it in folders, sorted by class. A user can then sort those thumbnails into the correct folder. You can then use those corrected thumbnanils to update the original labels.