islets 0.7.5

Features

One of our most used tools is the _’’roi examiner’’_ for live interaction with the ROIs and their traces within a jupyter notebook.

We have a similar app to examine line scans.

For examine detected events, one at a time, we also have a app.

We have also built a dashboard for fast intreaction with our storage filesystem. Given a folder, it finds all processed recordings in it and its subfolders, collects metadata and presents it in a table form. It further enables entering of the experimental protocol, and additional data, which are then also searchable. It also provides a link to an automaticaly generated notebook for a brief glimpse into actual results of an experiment. See demo on youtube (https://youtu.be/tj4TjL_PJ1Q).

Installation

We are working on an easy way of installation. For this purpose we use poetry as install tool. However, there will be ready-to-go packages available on PyPI via pip. For easy deployment, there will be a docker image as well. Documentation will be updated as soon as it is ready.

Docker

A dockerfile is included in the root of the framework. It contains everything to run python code in the base environment. It can be built with the following command:

docker build -t ctn_server .

If you do not want to build it yourself there is a prebuilt version on docker-hub. It can be pulled simly by:

docker pull hannsen/cell-tissue-networks_server:latest

As an example, to run the server with custom data and access it in a shell you can use it like this:

docker run -it -v /path/to/real/data:/data:rw hannsen/cell-tissue-networks_server:latest /bin/bash