Specimen's microarraysconsist of paraffin blocks in which separate tissue cores are assembled in array fashion to allow histological analysis. OpenSpecimen allows enables the creation of such specimen arrays with existing specimens to be tracked, processed, and created into slides.

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Specimen array supports below features:

1. Create a Specimen Arrayspecimen array
2. Create slides
3. Add events
4. Export array details
5. Import array arrays in bulk

Video

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Expand

Go to the home page and click on the ‘Arrays’ card. From the array’s list page, click Click on the ‘+ Create’ button Image Removed from the array's list page. Image Added Enter all valid details and click on the ‘Create’ button. Expand title Fields on 'Create Array' page Fields Mandatory? Description Name Yes Name of the array. Dimension (in mm) No Dimensions of the array. The dimensions are to be set in order Length X Width X Thickness (L X W X T). Capacity Yes The capacity of the array in terms of how many cores it can hold. The order to be followed is Rows X Columns. Labeling Scheme Yes Indicates the position labels, e.g., Alphabets Uppercase, Numbers : (A, 1).  The order to be followed is Rows X Columns.  Core diameter (in mm) Yes The diameter of the cores. Created by Yes It picks up the current user details  details by default. Creation Date Yes Picks up the current date by default. Quality No Indicates the quality of the array: Acceptable/ Not Acceptable/ Not Specified. Status Yes You can save the status as 'Draft' to ensure the array you created is fine. And then Once verified, you can come back and change the status to 'Completed .' '. Comments No You can add any additional comments in the field.

Add Specimens to Cores

Remove

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Specimens from

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Cores

Create Slides

The specimen array can be processed into slides.

Add

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Events

Once the slides are created, lab users might perform different analyses on the cores, like staining, and capture the details of the test results.

To do this, you can create new array events using 'Custom Forms' and attach them at the 'Specimen Array Event' or 'Specimen Slide Event' level, depending upon the level at which the information is to be entered. Check the 'Show In Grid' option for a field that should be displayed in the overview. In the below example, 'Stain Type' is shown in the grid.

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Edit Array Event

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Delete Array Event

Suppose you accidentally added the 'Staining Event' accidentally and wish to delete the entire event. This can be done by going to the 'Events' tab.

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In front of every event, there is a 'Delete' icon. You can delete the event from here for all the cores altogether.

Export

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Cores Detail and

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Map

Array details and array map can be exported as a CSV file with all details of the specimens used in the array. To export details, click on or ‘Export Cores Detail’ button and export the core map. Click on the ‘Export Cores Map’ button from the array’s overview page.

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Import Array

Arrays can be imported in bulk using the CSV import option from the main array list page (Arrays > Import > Arrays→ Import → Arrays). More information on Bulk Import of Arrays: Array CSV

This is useful for uploading legacy data.

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Sample CSV

Download

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When the specimens are added to the array, a specimen array event is added to each specimen present in the cores. All the details related to the array can be queried through the query interface of OpenSpecimen.

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