MultiSEM Workflow Manager is a third-party software that provides several important workflow management functionalities for Zeiss MultiSEM 505 microscope. It was written and tested with MATLAB R2017b, but a newer version of MATLAB before GUIDE deprecation should also work.

To start using the workflow manager, simply run msemRealTimeRetakeManager.m, select the experiment folder generated by the MutiSEM microscope (folder name ended with time-stamp), and a target folder to hold temporary results. msemRealTimeRetakeManager.m continuously probes experiment_log.txt in the experiment folder to determine whether a new section has been imaged, upon which carries out a collection of data validation tests (including file inventory, overlap test etc.), and saves the validation results to the temporary result folder.

In addition to the real-time mode, you can also run msemPostProcessingRetakeManager.m, which can work at the wafer folder level (one level up from the experiment folder).

The workflow manager can be configured to send out email alert whenever an unexpected error or workflow interruption occurs. To set up the email alert:

• Open RealTimeManager/send_email_alert.m, and configure the email server that sends out email by modifying all the setpref lines.

• Add the email addresses of the email alert recipients to alert_recipients.txt. One line for each recipients

• When running msemRealTimeRetakeManager.m, select send email notification when prompted.

To visualize image quality score, run msemQualityMapViewer.m and select the temporary result folder. You can click on the color-coded thumnail images in the pop-up window to open the full resolution EM images at the location clicked. you can also select a different section or adjust the apperence of the colormap by changing the options in the control-pannel. In the end, you can flag the section as to "keep" or to "retake" by clicking the radio buttons at the lower-right corner of the control pannel and leave the reason of retake for future references. The selections and comments will be included in the final html report.

The workflow manager includes a light-weight alignment module that roughly aligns the images using affine transform to detect out-of-target sections. To do that, run msemAlignOverviewStack.m, select the reference image in any of the some-experiment-folder/overview_imgs folder and wait the alignment program to finish. The algined stack is saved to temporary-result-folders/aligned_overviews.

Run msemGenerateHtmlReport.m to genrate a tablized summary of the workflow manager results for the datasets.