LSM Scan Uploader

This is a repository for accessing the source codes for the interface used in the ABA project at the Max Planck Institute for Multidisciplinary Sciences, Göttingen. This is a Python script that can be used to upload LSM scan images and metadata to an Amazon S3 bucket and a CaosDB server, respectively. It is designed to work with light sheet microscopy files, two photon images and CT scans.

Prerequisites

• Python 3.6 or higher
• pip package manager
• os, urllib, subprocess, json, datetime, streamlit, caosdb, time, logging, threading, io, urllib3, boto3, botocorepackages

Use pip install package_name to install all these packages)

How to Use

1. Open the terminal or command prompt.
2. Clone or download the repository and navigate to the project directory.
3. Run python MainProgram.py.
4. Enter the required information when prompted (sample ID/barcode, image and metadata paths, etc.).
5. Wait for the program to finish uploading the images and metadata.

Credits

This web application was developed, tested, and maintained by Ajinkya Kulkarni at the Max Planck Institute for Multidisciplinary Sciences, Göttingen.

License

This project is licensed under the GNU General Public License v3.0 - see the LICENSE file for details.

Contact

For more information or to provide feedback, please visit the project repository or contact the developer directly.