User Manual and annotation editor Image stack converter...1 Plate format will be automatically recognized after the stack is selected. 2 Icon visible in list view 3 Icon visible in

INPutImage stack converterand annotation editorUser Manual

cytiva.com

http://cytiva.com

Table of Contents

1 Important user information ................................................................................................................ 3

2 Introduction ......................................................................................................................................... 4

3 Using INPut to convert files ................................................................................................................ 53.1 Conversion of DeltaVision/OMX files ........................................................................................................................................... 63.2 Conversion of PerkinElmer Operetta/Columbus files ........................................................................................................... 12

4 Using the INPut Annotation Editor .................................................................................................... 154.1 Overview .................................................................................................................................................................................................. 164.2 Access the INPut Annotation Editor ............................................................................................................................................ 184.3 INPut Annotation Editor options .................................................................................................................................................... 19

Table of Contents

2 INPut User Manual 29639106 AA

1 Important user information

Typographical conventionsSoftware items are identified in the text by bold italic text.

Hardware items are identified in the text by bold text.

In electronic format, references in italics are clickable hyperlinks.

Notes and tipsNote: A note is used to indicate information that is important for trouble-free and optimal use of

the product.

Tip: A tip contains useful information that can improve or optimize your procedures.

1 Important user information

INPut User Manual 29639106 AA 3

2 Introduction

Application overviewINPut is a tool for converting image datasets into a format compatible with IN Carta™ analysis soft-ware. INPut also allows users to annotate .xdce stacks acquired on IN Cell instrumentation or gener-ated by the INPut converter.

INPut accommodates datasets acquired on or exported from:

• DeltaVision™ or DeltaVision OMX™

• PerkinElmer Operetta/Opera/Columbus

INPut main windowThe image below shows the initial view of the INPut main window.

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Part Description

1 Format drop-down list Allows selection of a format to convert.

2 Expand/Collapse button Expands/collapses image conversion log window.

3 Browse button Opens file/folder browsing dialogue.

4 Convert button Converts selected files into .xdce stack(s).

5 Cancel button Cancels current conversion operation.

6 Annotate button Opens INPut: Annotation Editor.

7 Help button Opens quick guide.

8 About button Opens information about software version.

9 Review panel Displays information during review step.

2 Introduction


3 Using INPut to convert files

About this chapterThis chapter contains instructions for converting files into xdce format.

In this chapter

Section See page

3.1 Conversion of DeltaVision/OMX files 6

3.2 Conversion of PerkinElmer Operetta/Columbus files 12

3 Using INPut to convert files


3.1 Conversion of DeltaVision/OMX files

File selection

Step Action

1 In the main window, select DeltaVision/OMX from the format drop-down list.

2 Click Browse.

Result:Files with one of the following file extensions appear in the Select Files to Convertdialogue box.

File extension Last post-processing step

DeltaVision/OMX All *.dv

Raw *_R3D.dv

Deconvolved *_D3D.dv

Projected *_PRJ.dv

SI Reconstructed *_SIR.dv

Aligned *_ALX.dv

Chromatically Corrected *_CRC.dv

3 Using INPut to convert files3.1 Conversion of DeltaVision/OMX files


Step Action

3 Select one or multiple files for conversion.

Note:Files can be filtered by file extension for display based on last post-processing step.

Tip:Hold Ctrl while clicking to select multiple individual files. Hold Shift while clicking toselect a range of files.

4 Click Open to import selected files for review.



ReviewDuring the review step the software displays groups of compatible files.

Files are grouped into plates based on dimensionality. Default plate dimensions depend on thenumber of files assigned to a plate. All files assigned to one plate have the same:

• magnification/pixel size

• image size

• number of channels

• number of z planes

• number of time-points



It is possible to modify the plate format or create a virtual plate format for images from a slide. Thefollowing table describes the possible user actions during the review step.

User Action Description

Display ToolTip with

• stack/dataset name

• image size/magnification

Hover the cursor over the plate heading in the review panel.

Change plate format Modify using drop-down menu under the plate heading. Imagefiles will automatically be assigned well information.

Exclude plate from conversion Deselect check box for the entire plate to the left of the plateheading.

Exclude individual files fromconversion

Deselect check box for the individual file assigned to a plate.

Change well assignment forindividual files

Modify row/column selection using drop-down menu to theright of the file name.

Change well assignment for agroup of files1

Follow the well-assignment procedure for multiple files,below.

1 Files will appear as fields within the selected well.

Modify well assignment for multiple files

Step Action

1 Left-click and hold the first file in the target range.

2 Drag the cursor up or down to select a range of files.

3 Release the left mouse button.



Step Action

4 Change the well assignment of the highlighted file in the selected range manually.

5 Right-click on any file within the selected group.

6 Select Assign to to assign all files in the selected group to the well chosen in step 4.



Conversion process overviewDuring the conversion process, the following information is displayed in the image conversion logwindow.

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Part Name Description

1 Overall progress bar Shows overall conversion progress

2 Plate progress bar Shows progress of current plate conversion

3 Log panel Shows details about conversion process, including finallocation path of .xdce stack files.

Convert selected files

Step Action

1 Click Convert.

Result:

Well assignments for each file are saved in annotation files, which are automaticallycreated for each plate.

2 To cancel the conversion, click Cancel.

Note:If the conversion is cancelled before it is complete, any newly generated files from theincomplete conversion will be automatically deleted.



3.2 Conversion of PerkinElmer Operetta/Columbus files

File Selection

Step Action

1 In the main window, select PerkinElmer Operetta or PerkinElmer Columbus from theformat drop-down list.

2 Click Browse.

3 Select a top level folder that contains the image stacks for conversion.

ReviewDuring the review step the software displays the stacks found in the Review panel.

The following table describes the possible user actions during the review step.

3 Using INPut to convert files3.2 Conversion of PerkinElmer Operetta/Columbus files


User Action Description

Display ToolTip with

• stack/dataset name

• image size

• magnification or pixel size depending ondata available

Hover the cursor over the plate heading in thereview panel

Exclude image stack from conversion Deselect check box for the image stack to the leftof the stack description

Conversion process overviewDuring the conversion process, the following information is displayed in the image conversion logwindow.

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Part Name Description

1 Overall progress bar Shows overall conversion progress

2 Plate progress bar Shows progress of current plate conversion

3 Log panel Shows details about conversion process, including finallocation path of .xdce stack files.



Convert selected files

Step Action

1 Click Convert.

2 In the Select Folder dialog box, specify the target output folder.

3 Click Select Folder.

Result:INPut initiates conversion of selected datasets into .xdce stacks.

4 To cancel the conversion, click Cancel.

Note:If the conversion is cancelled before it is complete, any newly generated files from theincomplete conversion will be automatically deleted.



4 Using the INPut Annotation Editor

About this chapterThis chapter describes the structure and use of the INPut Annotation Editor tool.

In this chapter

Section See page

4.1 Overview 16

4.2 Access the INPut Annotation Editor 18

4.3 INPut Annotation Editor options 19

4 Using the INPut Annotation Editor


4.1 Overview

IntroductionThe Annotation Editor tool allows the user to create custom plate layouts to store information abouteach well within a plate. Information about the content of each well can be typed directly into theAnnotation Editor widow, or pasted from a spreadsheet.

The annotation information created using the Annotation Editor will be accessible in future versionsof IN Carta™

INPut Annotation Editor main windowThe following image shows the initial view of the INPut: Annotation Editor main window. The iconsare described in the table below.

Icon Description

Create new annotation file by selecting a predefined sample format or entering acustom format (rows/columns) for the sample.

Create new annotation based on an .xdce stack.1

Open existing annotation file for review/edit.

4 Using the INPut Annotation Editor4.1 Overview


Icon Description

Save annotation file.

Save annotation as a new file.

Switch to plate view.2

Switch to list view.3

Sort list by row (default) or column.

Add new annotation type selected from a list of predefined descriptors or customnamed.

Remove last annotation column added.

1 Plate format will be automatically recognized after the stack is selected.2 Icon visible in list view3 Icon visible in plate view

4 Using the INPut Annotation Editor4.1 Overview


4.2 Access the INPut Annotation Editor

Step Action

1 In the INPut main window, click Annotate.

Result:The INPut: Annotation Editor window opens.

2 Navigate back to the INPut main window by clicking the X in the upper right corner of theINPut: Annotation Editor window.

Note:Save any open annotation file before closing the Annotation Editor.

4 Using the INPut Annotation Editor4.2 Access the INPut Annotation Editor


4.3 INPut Annotation Editor options

Predefined sample formatsThe following images shows the specimen holder sample format choices available for new annota-tions.

4 Using the INPut Annotation Editor4.3 INPut Annotation Editor options


Annotation descriptorsThe following image shows the annotation descriptors available when adding new columns. Customcolumns are named Custom by default and can be renamed by the user.

Editing contentAnnotations can be edited by directly typing content in the wells. Edits can also be performed forsingle or multiple wells according to the following table.

Edit User action(s)

Select multiple wells Left-click and hold while dragging over the target wells.

Repeat information from thetop selected well into multipleselected wells below

Right-click selected wells (including the source well) and chooseFill down from the drop-down menu.

Copy highlighted regions(single or multiple columns)

Right-click selected wells and choose Copy region from thedrop-down menu.

Use the keyboard shortcut Ctrl+C.

Paste previously copiedregions at cursor position

Right-click on one well and choose Paste from the drop-downmenu.

Use the keyboard shortcut Ctrl+V.



View

List View (default) Plate View

In list view, descriptors are shown as column headings. Sort the data in list view by clicking the sort

icon ( ) and choosing column or row.

In plate view, each descriptor is shown in a sample layout.



cytiva.comCytiva and the Drop logo are trademarks of Global Life Sciences IP Holdco LLC or an affiliate.

DeltaVision, DeltaVision OMX and IN Carta are trademarks of Global Life Sciences Solutions USA LLC or an affiliate doing business as Cytiva.

All other third-party trademarks are the property of their respective owners.

© 2020 Cytiva

Any use of INPut is subject to Cytiva Standard Software End-User License Agreement for Life Sciences Software Products. A copy of this Standard Software End-User License Agreement isavailable on request.

All goods and services are sold subject to the terms and conditions of sale of the supplying company operating within the Cytiva business. A copy of those terms and conditions is available onrequest. Contact your local Cytiva representative for the most current information.

For local office contact information, visit cytiva.com/contact

29639106 AA V:1 11/2020

http://cytiva.com

http://cytiva.com/contact

Documents

User Manual and annotation editor Image stack converter...1 Plate format will be automatically recognized after the stack is selected. 2 Icon visible in list view 3 Icon visible in