Instruments - Auto-import Pipeline
==================================

Crick's Advanced Light Microscopy (CALM) STP
-----------------------------

There are a few instruments that have implemented an autoimport pipelines. 

Olympus Slidescanners
---------------------
The Olympus Slidescanners are connected to Nemo storage where OMERO server can access.
Currently CALM STP provides a full service such that we will scan your slides for you using the Olympus Slidescanners.

Step-by-Step
------------
#. Please order the slide service through PPMS
#. Please take the slides to SW312.
#. We will scan the slides for you.
#. A snapshot of your images will be automatically backup by Nemo every night, import to OMERO will occur after that.

Confocal NL5
------------

Step-by-Step
------------
The Confocal NL5 is connected to Nemo storage through a Cache PC. OMERO server will periodically check whether there is any new data on the Cache PC. It will then move them to Nemo Storage.

#. Setup the instrument to acquire your images and save them on Z drive ``Z:\ome-tiff\<your crick user_id>``
      * example: for John Smith with crick user_id smithj, save it under ``Z:\ome-tiff\smithj\``
#. For each new aquisition, please create a new folder under your crick user_id folder.
      * example: ``Z:\ome-tiff\smithj\2025-10-20_NurseP_mouse_tumour\``
#. A snapshot of your images will be automatically backup by Nemo every night, import to OMERO will occur after that.


Experimental Histo-Pathology (EHP) STP
--------------------------------------

Zesis Axioscan
--------------
The Zesis Axioscan is connected directly to Nemo storage. OMERO server will periodically check whether there is any new data on the Zesis Axioscan Nemo folder. 
It will then import them when after a snapshot backup of your images is taken by Nemo.

Step-by-Step
------------
#. Setup the instrument to acquire your images and save them on O drive ``O:\<your crick user_id>``
      * example: for John Smith with crick user_id smithj, save it under ``O:\smithj\``
#. For each new aquisition, please create a new folder under your crick user_id folder.
      * example: ``O:\smithj\2025-10-20_SangerF_mouse_tumour\``
#. A snapshot of your images will be automatically backup by Nemo every night, import to OMERO will occur after that.



Akoya PhenoImagerHT Vectra Polaris
----------------------------------
The Akyoya PhenoImagerHT Vectra Polaris is connected directly to Nemo storage. However, the acquistion software saves that to the D Data Drive. 
An automatic backup program will be triggered at 6am every morning to transfer all the new data to Nemo Storage.
OMERO server will then import them after a snapshot backup of your images is taken by Nemo.

Step-by-Step
------------
#. Setup the instrument to acquire your images and save them on D drive ``D:\<your crick user_id>``
      * example: for John Smith with crick user_id smithj, save it under ``D:\smithj\``
#. For each new aquisition, please create a new folder under your crick user_id folder.
      * example: ``D:\smithj\2025-10-20_DarwinC_mouse_tumour\``
#. An automatic backup program will be triggered at 6am every morning to transfer all the new data to Nemo Storage.
#. A snapshot of your images will be automatically backup by Nemo every night, import to OMERO will occur after that.

Akoya PhenoImagerHT Vectra Polaris Analysis Platform
----------------------------------------------------
#. To be announced 

Lunaphore_COMET
---------------
#. To be announced 


Contents:


.. toctree::
   :maxdepth: 1

    import
    instruments
    access