Scanco User Instructions - Revision history

Erica.Baldesarra: /* Workstations and Scanco Server microCT Cluster */

2025-12-12T17:50:30Z

Workstations and Scanco Server microCT Cluster

← Older revision		Revision as of 17:50, 12 December 2025
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	You also have the option of saving the connection details. Hit <code>Save</code> or <code>Save As...</code> to save to a destination of your choice (e.g. Desktop). From there, double-clicking the file will attempt to start the connection.		You also have the option of saving the connection details. Hit <code>Save</code> or <code>Save As...</code> to save to a destination of your choice (e.g. Desktop). From there, double-clicking the file will attempt to start the connection.

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			=== Remote File Transfer ===

			There are many ways to transfer files from the remote systems to your local computer. I will outline a few below that are more specific to the Scanco System. There are others like FileZilla that may work better, especially if you are used to using these methods. See [https://wiki.filezilla-project.org/FileZilla_Client_Tutorial_(en) FileZilla tutorial] for how to use that. (NOTE: firewall restrictions on the system may block FileZilla connections currently.)

			Once connected remotely to a ''workstation'', any file can be transferred from the file browser to the workstation itself. From there, you can transfer the files to your local computer. The Process is as follows:

			1. Connect [[Scanco_User_Instructions#Remote_Connection_to_Workstations\|remotely]] to the workstation.

			2. Navigate to and open the [[Scanco_User_Instructions#File_Browser\| File Browser (Scanco)]]

			3. Locate the file(s) you would like to download

			4. Select/highlight the files, and right-click on your selection

			5. Click 'Download' from the drop-down and choose a destination folder on the workstation (you may want to create your own)

			6. Once the files are downloaded to the remote workstation, right-click the directory and click 'Copy' (or, select it and use the <code>Ctrl + C</code> keyboard shortcut)

			7. Navigate back to your local computer, and paste the contents where you would like them stored

			[[File:File_download.png\|400px]]

			If connected to the Scanco Server, you are able to skip a few steps from above. This is because the files are stored physically on the server, whereas the workstations [[Scanco_User_Instructions#Mappings\|virtually]] access those files. The process for this is:

			1. Repeat steps 1-3 above, connecting to the Scanco Server instead

			2. Identify the '''physical path''' of the file(s) you would like to copy.

			3. Navigate to Windows File Explorer. Either copy the physical path of the file(s) you would like to copy or navigate to their location

			4. Now repeat the last two steps above: right-click the directory and click 'Copy' (or, select it and use the <code>Ctrl + C</code> keyboard shortcut)

			5. Navigate back to your local computer, and paste the contents where you would like them stored

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			==== Batch File Transfer ====

			This process also allows you to batch move/copy files on the Scanco Server. A useful pipeline for file transfer may be (once logged into the server):

			1. Create a temporary file directory on the server (on the desktop or in the documents folder, for example).

			2. Identify the locations of the files you would like to transfer (the [[Scanco_User_Instructions#File_Browser\|file browser]] can help with this: right-click on the file and select 'Copy Physical Path')

			3. Create a bash (.sh) script which iterates through those files, and copies them to the directory you made in step 1.

			4. Run this script using the [[Scanco_User_Instructions#Console\|console]] or cmd.exe on the server

			5. Locate the directory you made in step 1 in File explorer (or on your desktop if that's where it was created)

			6. Right-click the directory and click 'Copy' (or, select it and use the <code>Ctrl + C</code> keyboard shortcut)

			7. Navigate back to your local computer, and paste the contents where you would like them stored


			You can also use the [[Scanco_User_Instructions#Data_Manager\|Data Manager]] to batch copy files to a directory on the workstation or an external drive that is connected. To do so (once logged in remotely):

			1. Open the Data Manager application from the application center

			2. Filter by Scan Group or sample name to find which files you would like

			3. In the operation option buttons, select 'Copy To'.

			4. Beside the 'Copy To' button, select 'Export To ...' to export the files to a folder on the computer, or select the drive to copy the files to.

			5. If you would like associated files rather than image files (e.g. logs, csv results, result PDFs...):

			Select 'IMA' under 'Selected Measurement'. Then, select which file types you would like to copy.

			6. Click 'Start' to begin the copy

			[[File:data_manager_copy.png\|700px]]

			NOTE: an ssh server is not currently active on the Scanco server, and therefore file transfer using command-line ssh connections (e.g. sftp, scp, rsync) cannot currently be authorized.

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Erica.Baldesarra: /* Mappings */ Elaborate on physical vs virtual paths

2025-11-18T22:33:19Z

Mappings: Elaborate on physical vs virtual paths

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	This tab displays the virtual-physical path mappings from the workstations to the Scanco Server. You can enter a virtual path into the <code>Virtual Path</code> text box to search for its associated physical path.		This tab displays the virtual-physical path mappings from the workstations to the Scanco Server. You can enter a virtual path into the <code>Virtual Path</code> text box to search for its associated physical path.

			All of the files origin is from the Scanco Server. The physical path relates to their location on that server. Their virtual path is the access point that the workstations use to retrieve those files remotely from the server. When running scripts and when logged into the Scanco Server directly, it is best to use the physical path. If accessing the files remotely from a workstation, the virtual path should be used.

	==== Files ====		==== Files ====

Erica.Baldesarra: /* Script Variables */ Add editable variable example

2025-11-18T18:57:06Z

Script Variables: Add editable variable example

← Older revision		Revision as of 18:57, 18 November 2025
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	We can think of variables as script parameters you can change in the GUI before running the script. These will be displayed to you in the bottom of the Tasks window below the dimension text boxes after you select your script.		We can think of variables as script parameters you can change in the GUI before running the script. These will be displayed to you in the bottom of the Tasks window below the dimension text boxes after you select your script.

			To have these editable values populate in the tasks window, select the parameter group from the drop-down. Then, select which 'item' in that group you would like to show (i.e. '1' for the first listed parameter in the Advanced window, '2' for the second...). Under <code>Label</code> input the name you would like to display to the user for entry. Finally, choose which type the input data should be and (if applicable) enter any range limits for it.

	[[File:variables_script_entries.png\|500px]]		[[File:variables_script_entries.png\|500px]]

			As an exmaple, the in-house script for printing parameters for autocontouring allows users to edit the filename. The parameter group is MISC, the item varies based on how the script is set up (9 in the example below), and the type is text input.
			It also has a boolean option that allows you to select between Trabecular and Cortical as the default saved <code>.gobj</code> file. These options are shown in the tasks window below.

			[[File:variables_example.png]]


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Erica.Baldesarra: /* Advanced Script Parameters */ Add advanced variable details

2025-11-18T18:47:10Z

Advanced Script Parameters: Add advanced variable details

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	=== Advanced Script Parameters ===		=== Advanced Script Parameters ===

			These can be adjusted to edit the expected <code>.gobj</code> or <code>.aim</code> file names, or specify a default segmentation threshold value/units, or other script-specific variable changes. Notably, the autocontour script requires MISC0-MISC5 to be set for the images you would like to contour. See the [http://www.scanco.ch Scanco website] for more specific variable details.

	[[File:advanced_script_entries.png\|500px]]		[[File:advanced_script_entries.png\|500px]]

Erica.Baldesarra: /* Tasks */ Update scripting link

2025-11-18T18:40:39Z

Tasks: Update scripting link

← Older revision		Revision as of 18:40, 18 November 2025
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	==== Tasks ====		==== Tasks ====
	This is the window where you can run your analysis [[~~Scripts~~\|scripts]], after you have drawn the appropriate contours. By clicking the buttons next to the parameter box (or F5), you can view the segmented parts of the image within the contours.		This is the window where you can run your analysis [[Scanco_User_Instructions#Scripting\|scripts]], after you have drawn the appropriate contours. By clicking the buttons next to the parameter box (or F5), you can view the segmented parts of the image within the contours.

	[[File:segment_show.png]]		[[File:segment_show.png]]

Erica.Baldesarra: /* Sample Registration */ Update scan groups link

2025-11-18T18:33:31Z

Sample Registration: Update scan groups link

← Older revision		Revision as of 18:33, 18 November 2025
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	To copy and paste sample names, you can now easily highlight the name with your cursor and click <code>Ctrl + C</code> to copy and <code>Ctrl + V</code> to paste.		To copy and paste sample names, you can now easily highlight the name with your cursor and click <code>Ctrl + C</code> to copy and <code>Ctrl + V</code> to paste.
	This application also now allows you to view and edit [[Scan Groups]].		This application also now allows you to view and edit [[Scanco_User_Instructions#Scan_Groups\|Scan Groups]].

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Erica.Baldesarra: /* Command-Line Scripting and IPL */ Add console instructions

2025-09-11T20:03:29Z

Command-Line Scripting and IPL: Add console instructions

← Older revision		Revision as of 20:03, 11 September 2025
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	=== Command-Line Scripting and IPL ===		=== Command-Line Scripting and IPL ===

	Any scripts stored on the Scanco server can be run from the command-line as well.		Any scripts stored on the Scanco server can be run from the command-line as well. To access the command-line on a Scanco workstation or the Scanco server,

			1. Open the Scanco Application Center
			2. Click <code>Tools -> Console</code>

	NOTE: IPL is not installed on the workstations themselves and cannot be run from their command-line.		NOTE: IPL is not installed on the workstations themselves and cannot be run from their command-line.

Erica.Baldesarra: /* Job Queue */ Add job queue picture and filter info

2025-09-11T19:53:08Z

Job Queue: Add job queue picture and filter info

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	=== Job Queue ===		=== Job Queue ===

	The Job Queue tool allows you to keep track of running Jobs (generally scripts you have run). Any task run from the Evaluation application will have an associated listed job in the queue. Images evaluated from a scan or scheduled scans will also have a job in the task list. This entry tells you its status (Running, Successful, Aborted, Failed), its job number and the type of job (IPL script, GPU evaluation, batch scan... etc). To see the job's associated log, you can right-click on its name in the queue list.		The Job Queue tool allows you to keep track of running Jobs (generally scripts you have run). Any task run from the Evaluation application will have an associated listed job in the queue. Images evaluated from a scan or scheduled scans will also have a job in the task list. This entry tells you its status (Running, Successful, Aborted, Failed), its job number and the type of job (IPL script, GPU evaluation, batch scan... etc). To see the job's associated log, you can right-click on its name in the queue list. The job queue can also be viewed from the Evaluation application under <code>Tasks -> History -> Job Queue </code>

	[[File:job_queue.png]]		[[File:job_queue.png\|500px]]

			You are able to filter the job list by any of its information: description, status, type... etc.

	=== Console ===		=== Console ===

Erica.Baldesarra: /* Modifying/Creating Scripts and Batch Scripting */ Add editing scripts gui info

2025-09-11T19:34:18Z

Modifying/Creating Scripts and Batch Scripting: Add editing scripts gui info

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 === Modifying/Creating Scripts and Batch Scripting ===
-User scripts (python and IPL) are stored at <code>@sns/[project#]/evalscript</code>. To use them in a custom script from the Evaluation Application Tasks window, click <code>Scripts -> Modify Scripts</code>. From here, you can either use a previous script template and change its variables or create a brand new script template. When copying an old script template, make sure to rename it to something new and click <code>Save as New</code> when you are done. To create a brand new script, click <code>New</code>
+User scripts (python and IPL) are stored at <code>@sns/[project#]/evalscript</code>. To use them in a custom script from the Evaluation Application Tasks window, click <code>Scripts -> Modify Scripts</code>. From here, you can either use a previous script template and change its variables or create a brand new script template. To use an old script as a template, select it from the list and click <code>Modify</code>. When copying an old script template, make sure to rename it to something new and click <code>Save as New</code> when you are done. To create a brand new script, click <code>New</code>.
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Erica.Baldesarra: /* Scripting */ Add scripting info

2025-09-11T18:03:14Z

Scripting: Add scripting info

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 Scanco provides some basic analysis scripts already and script templates. The description for how to use these is found [https://www.scanco.ch/scanner-support.php| on the Scanco site.]
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 === Modifying/Creating Scripts and Batch Scripting ===
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