Minimal dataset & code for proof of concept - Argoslide - Fiji - OMERO

An open-source workflow for assessing light microscope performance using a single micropattern.

Romain Guiet, Thierry Laroche, José Artacho, Nicolas Chiaruttini, Olivier Burri, Arne Seitz

The growing need for reliable quantitative measurements in light microscopy has been identified by the community recently and led to the creation of an initiative called  Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy (QUAREP-LiMI). One of the aims is to push for the creation of simple, direct, reliable and widely adoptable instrument quality controls. This serves for defect detection, continuous proof of the instrument's ability to reliably produce quality imaging data, and the possibility to compare performance across devices. 

By lowering the learning curve for facilities and laboratories through simple robust protocols and as-automated-as-possible open source image processing, we produced a workflow for the acquisition and measurements of typical light microscope metrics using a single pattern from a commercially available ArgoLight-SIM slide. Through a fully automated workflow in Fiji, we can measure axial resolution (FWHM ), inter-channel co-registration (Pearson's Correlation Coefficient), field uniformity (local intensities) and field distortion (comparing spatial localization with respect to a simulated pattern) at multiple positions across the field of view, in a single image. 

Moreover, in order to ease bookkeeping, an OMERO database is used as a backend to store the acquired images, metadata, as well as the resulting metrics and reports. These reports in turn can be used within OMERO Parade to follow instrument performance changes. This workflow is built on open-source software and will facilitate  the assessment of instrument quality over time with minimal effort.

  == INPUTS ==
  Images to upload and analyse , a template image to find rings ( available : https://doi.org/10.5281/zenodo.6597338)
  OMERO : 
   - an active user 
   - a project , please project ID at "argoslide_project_ID" (see below)
   - a dataset, name .LSM980.

  == OUTPUTS ==
  Upload images on OMERO, 
  Compute metrics and add them into an OMERO table
  Add tags to uploaded images

  = DEPENDENCIES =
   - omero-simple-client.jar : https://github.com/GReD-Clermont/simple-omero-client
  update site :
   - IJ-OpenCV 
   - Multi-Template-Matching

基于单微图案的光学显微镜性能评估开源工作流

Romain Guiet, Thierry Laroche, José Artacho, Nicolas Chiaruttini, Olivier Burri, Arne Seitz

近年来，光学显微镜领域的学界愈发亟需可靠的定量测量手段，由此催生了光学显微镜仪器与图像质量评估及可重复性倡议（Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy，简称QUAREP-LiMI）。该倡议的核心目标之一是推动建立简便、直接、可靠且易于广泛推广的仪器质量控制方案，用于设备故障检测、持续验证仪器稳定产出高质量成像数据的能力，以及实现不同设备间的性能对比。

我们通过简便稳健的实验方案与尽可能自动化的开源图像处理流程，降低了设施与实验室的学习门槛，基于商用ArgoLight-SIM载玻片的单图案，开发出一套可采集并测量典型光学显微镜性能指标的工作流。借助Fiji中的全自动化工作流，我们可在单张图像中，针对视场内的多个位置测量轴向分辨率（半高全宽，FWHM）、通道间配准精度（皮尔逊相关系数，Pearson's Correlation Coefficient）、视场均匀性（局部光强）以及视场畸变（对比空间定位与模拟图案的偏差）。

此外，为简化档案管理，我们采用OMERO数据库作为后端，存储采集到的图像、元数据以及最终生成的性能指标与分析报告。这些报告可通过OMERO Parade追踪仪器性能的动态变化。本工作流基于开源软件构建，可帮助用户以极低的工作量实现仪器质量的长期评估。

== 输入 ==
需上传并分析的图像，用于查找圆环的模板图像（获取地址：https://doi.org/10.5281/zenodo.6597338）
OMERO相关要求：
- 活跃的用户账号
- 一个项目，请将项目ID填写至"argoslide_project_ID"（详见下文）
- 一个数据集，命名为.LSM980。

== 输出 ==
将图像上传至OMERO
计算性能指标并将其添加至OMERO数据表
为上传的图像添加标签

= 依赖项 =
- omero-simple-client.jar：https://github.com/GReD-Clermont/simple-omero-client
更新站点：
- IJ-OpenCV
- Multi-Template-Matching