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Table of Contents

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.

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  1. Creating specimen array

  2. Creating slides

  3. Adding events

  4. Export array details

  5. Import arrays in bulk

Video

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Create Array

Expand
titleExpand to Create Array

  • 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.

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titleFields of 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.

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Expand

  • 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 Time Finished 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 Time Finished. 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

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Suppose you accidentally added the 'Staining Event' 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 Cores Detail and Map

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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). More information on Bulk Import of Arrays: Array CSV

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