====== Microscope Calibration Project ======

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===== Introduction =====

Microscope Calibration is both, a [[https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/working-groups-list/joint-4dn-analysis|Joint 4D Nucleome Analysis project]] and a key aim of the [[https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/working-groups-list/imaging-data-standards-wg|Imaging Data Standards]] workgroup. Calibrating microscopes across a large user group like the 4DN consortium is difficult in its own right and not often done. We attempt to find a way to do calibration that is easy enough to be efficiently implemented in the lab.

Calibration has at least three major components to it, optical performance, photons-in/photons-out ratios and linking the calibration data in a reasonable way to the data. These components are mirrored in the major headings of this page.

Calibration is a complex topic and while the Imaging Data Standards workgroup has proposed and is doing development of a test tube tool for light calibration, the Joint 4D Nucleome Analysis Project on Microscope Calibration starts with Optical Calibration.

===== Aim =====

==== Stage 1: Optical Calibration using Tetraspeck beads and PSFj ====

This is the current (October 2017 to ~March 2018) project part. The aim is to establish a database with monthly recorded multi-color bead stacks from microscopes within the 4DN consortium. Bead stacks are used for two reasons:

  - To create a reference data set that can be used to compare results from the microscope of any specific user against other comparable microscopes.

  - As an easy sample with minimal variability to work with DCIC on metadata organization and data upload.

Over the duration of this project we will expand the number of contributors. We start with the Grunwald lab and DCIC (aim: develop the technology and infrastructure backbone), step one expansion will include a small set of optical technology development labs (aim: beta test the system), in step two we reach out to image production labs (aim: calling the afford) and in step three will address everyone using a microscope in the consortium.

**IF YOU WANT TO CONTRIBUTE TODAY:**  Everybody is welcome and invited to join this project at anytime. Please download the one-page protocol below (under "Optical Calibration Documents") to get started. Contact me (david.grunwald@umassmed.edu) with questions and start taking bead stacks! The above steps are a lower bound: we will bother you to contribute at some point, we welcome you at any time!

===== Optical Calibration - Definition and Resources =====

(under development)

As working definition we refer to optical calibration as the monitoring of imaging performance of a microscope. We use a sample that is aimed at fluorescence microscopy of diffraction limited, or close to diffraction limited signals. More details can be found in the documents linked to this section.

===== Metadata Tier Level - Definition and Resources =====

(under development)

===== Light flow Calibration - Definition and Resources =====

(under development)

===== Microscope Calibration - Literature =====

==== Optical Calibration Documents ====

  * [[https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/working-groups-list/imaging-data-standards-wg/microscope-calibration-project/literature|LITERATURE]]

  * [[https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/working-groups-list/imaging-data-standards-wg/microscope-calibration-project/optical-calibration-documents|Optical Calibration Documents]]

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