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AddingSlidestotheinFormQueue.md

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5.8.5. Adding Slides to the inForm Queue

5.8.5.1. Description

The inForm Queue was designed to send processing tasks to the virtual machines for batch processing images from slides set up in the AstroPath Pipeline directory structure. The code processes the images from the flatw_path created by the image correction module (5.7.). The user adds projects to the queue located in the project's *\Clinical_Specimen_XX\upkeep_and_progress folder. Once projects are added, the mergeloop module automatically transfers the projects to the main queue located at the <mpath>\across_project_queues\vminform-queue.csv, where the vminform code automatically dessiminates tasks to the servers. Typically, users will only interface with the inForm_queue.csv in the project's *\Clinical_Specimen_XX\upkeep_and_progress folder. The most recent projects used are recorded in the samples_summary.xlsx spreadsheet (also in the upkeep_and_progress folder).

5.8.5.2. Important Notes

  • Once the pipeline properly finishes the imagecorrection module for a slide and correctly registers the MergeConfig_NN.xlsx file for that slide it will intialize the inForm_queue.csv with a line for each slide - antibody pair. If a slide - antibody pair is not intialized it means either the image corrections are not finished or the MergeConfig_NN.xlsx file was not set up\ not set up correctly. Directions on that file are located here.
  • Only manually add rows when it is time to rerun a project. The code search for algorithms in the \Clinical_Specimen_XX\tmp_inform_data\Project_Development folder. For saftey reasons, the code will not search subfolder and the input is case senstive. Additional details on saving algorithms can be found here.
  • For antibodies with multiple segmentaions, there will be a second row labeled <Antibody>_2. Usually this is done when a marker can express on different sizes of cells (like PDL1), be sure to keep track of which algorithm was used for the large cells and which for the small cells.

5.8.5.3. Instructions

  1. Navigate to the *\Clinical_Specimen_XX\upkeep_and_progress folder.
  2. Open the InForm_Queue.csv file and fill out the columns
    • this file has the following columns: Path, Specimen, Antibody, Algorithm, Processing
    • Path: The path up to but not including the specimen folder or \\<Dname>\<Dpath> (described here)
      • E.g. \\bki04\Clinical_Specimen_2
    • Specimen: The name of the specimen to be analyzed
      • The image data to be processed should be located in an <Path>\<Specimen>\im3\flatw folder
      • E.g. M1_1
    • Antibody: The antibody name that will be processed.
      • All data will be exported into a <Path>\tmp_inform_data\<Antibody> subfolder
      • E.g. CD8
    • Algorithm: The name for the project to do the processing include the file extension
      • The project should be location in a <Path>\tmp_inform_data\Project_Development folder for the code to be able to find it
      • Only the Project_Development folder will be search, the search is not recursive. Subfolders will not be searched for the algorithm
      • E.g. CD8.ifp
    • Processing Location: Where the slide is being processed
    • Start: The time that the processing started, this is updated by the code and should be left blank
  3. Save and close the file

NOTE: you only need to fill out the Algorithm column for the first time a slide - antibody pair is run. To rerun a slide - antibody pair add it to a new row with the new project (be sure to fill out the Path column as well).