automated data collecting

Question

[CONNOR]

Hey everyone, I am trying to set up an automated data collection system for my lab. What tools, practices, and strategies have some of you tried to accomplish this? My highest priority is to organize microscopy images and their metadata.

right now, I have a database that contains information about each sample, features extracted from microscope images, and the image's location in a cloud storage bucket as well as what stains were used. I established a naming convention so that I know what plate and well each image comes from, but still have to manually input data they enter from a google sheet. the images are in a folder synced regularly with the cloud bucket.

any advice or feedback would be greatly appreciated.

thanks!

[Jean-Karim Heriche]

This is a question for the image.sc forum.

Answer 1

[Alex Reynolds]

One search term that might be useful is "LIMS", short for Laboratory Information Management System.

These systems generally help with data generation (e.g., pipelining), as well as storage and retrieval of said data, later on.

You have pieces of a LIMS of a kind, albeit with a lot of manual processes. Not all LIMS are the same for all labs. Other LIMS focused on imaging or microscopy may help provide some formalized automation and centralization of your variety of data.