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

Features

Specimen array supports below features:

Create a specimen array
Create slides
Add events
Export array details
Import arrays in bulk

Video

Create Array

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Navigate to ‘Arrays’ from navigation menu.
Click on the ‘+ Create’ button from the array's list page.

Enter all valid details and click on the ‘Create’ button.

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 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. 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

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Click on the ‘Array Map’ icon from the left side menu.
Scan specimen labels delimited by comma, tab, or newline and click on the ‘Assign Cores’ button.

You specify the location within the array for each specimen, e.g., put position like (3,1)999 (specimen label). Some cells within the array can be left blank. You can put extra commas or click on the '+' mark within the array map to skip positions.
Once the array is marked as completed, the array map cannot be changed to add or remove other specimen cores.

Go to the array's overview page, click on the ‘Edit’ button and change the array's status to ‘Completed’.

The system adds the ‘Specimen Array Event’ to the specimens added in the cores. You can view the event added under the ‘Recent Events’ list on the specimens overview page.

Remove Specimens from Cores

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Check the checkbox of any cores to be removed from the array.

Click on the ‘Remove Cores’ button.

The ‘Remove Cores’ button will appear only if the checkbox of any core to be removed is checked.
You can remove cores only if the array is in 'Draft' mode.

Create Slides

The specimen array can be processed into slides.

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Click on the ‘+Create Slides’ button from the overview page of the array.

Specify the number of slides to be created and click on the ‘Next’ button.

Enter slide names and thickness of the slides to be created and click on the ‘Create’ button.

The created slides list will appear on the array’s overview page under the ‘Slides’ section.

Add 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.

More information on creating and attaching the custom form: Custom Form

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Once the custom form is created and attached at 'Specimen Array Event'/ 'Specimen Slide Event', click on' Add Event' from the main page of the array or slides.
Choose the event from the dropdown and enter event details for all cores in the array.

After adding an event, the event appears on the overview page on the right-hand side.

Clicking on the event shows the overview as below:

Edit Array Event

In case you wish to edit the event details, follow the steps:

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Clicking on the event on the right-hand side, go to the overview page.
The details are visible in the grid, based upon the form fields that have 'Show In Grid' selected. In this case, it is the stain type only. It appears as a hyperlink. If you wish to display all the details in the grid in the custom form, check 'Show In Grid' for all the fields.

Click on the stain type. This will lead you to the edit event page for that particular core:

These details can be updated, and then click 'Save'.

Delete Array Event

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

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

Export Cores Detail and 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.

Import Array

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

This is useful for uploading legacy data.

Sample CSV

Download

Querying Array Details

When the specimens are added to the array, 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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The below filters can be viewed under the 'Specimen Array Event' filters on the left-hand side. Using these, you can apply conditions to the array.

The data can be viewed from 'View Records' by selecting the columns under 'Specimen Array Event'.

Note:

It is not possible to query the Specimen Array Status.

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