Leica SCN400 user guide July 2013 Location: 55+2, tel: 4.55.25 General workflow 1. Scanner ON 2. PC ON 3. Leica SCN400 Client ON 4. Slides in carriers carriers in hotels 5. Insert hotels (access to open door) 6. Choose scanning mode Basic mode Batch mode with overviews Batch mode w/o overviews Interactive mode 48 slides (1 hotel) > 48 slides >48 slides or slide series with different scan protocols (max 48 z-stack, special options, slides with different scan protocols slides/protocol) load slides (select 1 hotel): advanced-autoloader tab advanced-autoloader tab advanced-autoloader tab overview select magnification assign scan protocol for each hotel import slide names select 1 hotel / carriers select scan areas select hotels define automatic file export scan (overview) (in configuration) rename (right click) select overviews only assign scan protocol for each hotel define scan protocol define file export scan (overview) select hotels assign scan protocol for each slide multi-scan (or scan) select scan areas scan (overview and scan) rename (right click) eject rename (right click) scan multi-scan (or scan) define file export eject file export multi-scan eject eject 7. Scanner OFF 8. Log OFF or PC OFF 1
Switch ON (It takes ± 10 min for initialization) (buffer storage stays ON) Scanner ON PC ON Log in as SCN400 Users (password: IREC2IP) and click on the ARROW. Start the program Leica SCN400 Client (Note : Help = F1) Log in : The scanner is ready when «Idle Idle» status is indicated. 2
Load slides Insert up to 4 clean slides (single slide format) into each slide carrier. Insert up to 12 slide carriers into each hotel. The hotel handles must be uppermost. Never open the door unless indicated by the system! 3
Scanning modes 1. Basic mode (1 hotel) The scanner is ready when «Idle Idle» status is indicated. Select 1 hotel and overview - Switch to the Acquire workflow step. - Select the Manual and Basic tab. - Click on Load slides and choose the hotel. The following message will appear. 4
- Open the door, insert the hotel and click on OK. An overview of all the slides (from all carriers) will appear automatically (± 1 min/carrier). Select scanning magnification - To assign the same magnification to all slides select several slides using the shift or ctrla function select the required magnification - To assign different magnifications to different slides: click on an overview thumbnail select the required magnification click on the next overview thumbnail Select scan areas Select overview thumbnails and select scan areas. Suggested areas will appear and can be modified for each slide with the tool bar at the right of the screen. 5
Optional: change slide names With the right-hand mouse key on the overview thumbnails, choose Rename and enter the desired name (for each slide). Define File export - Click on Change FileExport path. 6
Press the Edit key to set up the file export options: Export after Overview and Scan: to export automatically. Remove after Export : raw data are deleted after file export (only if export after overview and scan selected). Export folder: change the pole of destination (ex: CARD, PNEU, MIRO, FATHcardio, ) \\dih.irec.ucl.ac.be\servedimages\pole. DO NOT BROWSE!! Compression quality : set 75-80% - Select all overview thumbnails using the shift key and select FileExport. 7
Scan To scan several slides: select the overviews to scan using the shift key (or ctrla) and select Multi scan. To scan 1 slide: select only one overview and press the Scan button. To interrupt the scan: click on Cancel scan queue. The progress of the scan will be indicated as follow (waiting, active, complete): Depending on the tissue size, it takes 2-5 min to scan 1 slide at 20x. 8
Eject the slides - Click on Eject. - Wait for the carrier to be ejected. - Select Advanced and the Autoloader tab. - Click on the Access button of the desired face to open the door. Shutdown the scanner if you are the last user See last page Close Leica SCN400 Client Log OFF 9
2. Batch mode with overviews (>48 slides) The scanner is ready when «Idle Idle» status is indicated. Insert hotels - Switch to the Acquire workflow step. - Select Advanced and the Autoloader tab. - Click on the Access button of the desired face. The selected face is now moved to the loading position and the message box is displayed. Now you can open the door of the autoloader. 10
The following message will be displayed: - Close the door of the autoloader and access the next face. Insert the hotels as described above. Select hotels and overview - For each hotel you want to scan, choose a Scan Protocol by clicking on the double arrow and by selecting it from the list of available scan protocols. 11
- Click on Confirm or drag and drop. The hotel is displayed in the Batch Mode window. Example for batch mode with two hotels confirmed: - Select Overviews only and click on Scan to have overview images. (The circle at the Scan button turns red). Select scan areas Select overview thumbnails and select scan areas. Suggested areas will appear and can be modified for each slide with the tool bar at the right of the screen. 12
Change slide names With the right-hand mouse key on the overview thumbnails, choose Rename and enter the desired name (for each slide). Define File export - In the main toolbar, go in Edit - Configuration - Options - File Export Press the Edit key to set up the file export options: deselect Export after Overview and Scan. deselect Remove after Export. Export folder: change the pole of destination (ex: CARD, PNEU, MIRO, FATHcardio, ) \\dih.irec.ucl.ac.be\servedimages\pole. DO NOT BROWSE!! Compression quality : set 75-80% 13
Scan To scan several slides: select the overviews to scan using the shift key and select Multi scan. To scan 1 slide: select only one overview and press the Scan button. To interrupt the scan: click on Cancel scan queue. The progress of the scan will be indicated as follow (waiting, active, complete): 14
Export In this scan mode, export has to be done manually. Select the images to export using the shift key (or ctrla), right-click and choose Start File Export - SCN. Note: if SCN is grey (unselectable), go back to Define File Export (deselect Export after overview and scan). When files are exported (ExportedOK), right-click and choose Delete ImageCollection. Eject the slides - Click on Eject. - Select Advanced and the Autoloader tab. - Click on the Access button of the desired face to open the door. 15
Shutdown the scanner if you are the last user See last page Close Leica SCN400 Client Log OFF 16
3. Batch mode without overviews The scanner is ready when «Idle Idle» status is indicated. Insert hotels - Switch to the Acquire workflow step. - Select Advanced and the Autoloader tab. - Click on the Access button of the desired face. The selected face is now moved to the loading position and the message box is displayed. Now you can open the door of the autoloader. 17
The following message will be displayed: - Close the door of the autoloader and access the next face. Insert the hotels as described above. Optional: import slide names. Open the Excel spreadsheet AutoNamingDefinitions. 18
Input the desired slide names into the column Slide Name. (A slide name has to be unique. In case of accidentally using a slide name more than once, the SCN400 software will automatically replace this name.) Store the modified spreadsheet under a new name. To import the list of slide names select the option Import Slide Names of the File menu. Choose a file and click on Open. The content of the AutoNamingDefinition file is displayed. Notes: - The dialog can be displayed again at any time by selecting the option Show Imported Slide Names. - To remove the auto naming list click the option Delete Imported Slide Names.) - An imported list remains only valid as long as the door of the autoloader has not been opened. Import the slide names again after opening the door. Define file export settings. Open Configuration in the menu bar, go to menu Options and select the submenu File Export. Export Type: select SCN Press the Edit key to set up the file export options: Export after Overview and Scan: to export automatically. 19
Remove after Export : raw data are deleted after file export (only if export after overview and scan selected). Export folder: change the pole of destination (ex: CARD, PNEU, MIRO, FATHcardio, ) \\dih.irec.ucl.ac.be\servedimages\pole. DO NOT BROWSE!! Compression quality : set 75-80% (note: The file size is halved by switching from 100% to 95%!) Save the new settings using the Save key. Close. Select hotels and scanning protocols Select Advanced and the Autoloader tab. If necessary, select the Batch Mode button in the Interactive Mode window to activate the Batch Mode. For the hotel you want to scan, choose a Scan Protocol by clicking on the double arrow and by selecting it from the list of available scan protocols. 20
The selected scan protocol is automatically displayed in the Scan Protocol dialog of the control tab area. So it is possible to check the settings of the selected scan protocol. Use the key to assign the selected scan protocol to all hotels at once. If the option Use suggested areas in the Scan Protocol dialog of the control tab area is activated, these areas will be taken as default. The Confirm button is now activated and the red question mark disappears. 21
Click on Confirm or drag and drop. The hotel is displayed in the Batch Mode window. Example for batch mode with two hotels confirmed: Individual hotels can be removed from the queue and the scanning order can be changed. Therefore click on the desired hotel. It will be highlighted. The most left hotel is scanned first. 22
Overview and scan Select Scan. (The circle at the Scan button turns red.) Overview of the 4 slides of the first carrier appears automatically (in the Manual tab). These 4 slides are then automatically scanned. The next carrier is then processed (overview, then scan), To interrupt the current scan: click the Scan button again. To continue an interrupted scan, click the Scan button once more. To abort a running scan, first click the Scan button to interrupt the scan and remove the current hotel window using the right-hand mouse key. Select the option Remove. The hotel in the batch active window can now be removed using the right-hand mouse key. Select the option Remove. If the hotel is not removed, you can continue scanning by clicking the Scan button once more. Eject the slides. Click on Eject. Click on the Access button of the desired face to open the door. Shutdown the scanner if you are the last user See last page Close Leica SCN400 Client Log OFF 23
4. Interactive mode (for 1 hotel) By switching to the Interactive Mode, a running batch can be interrupted, for example to scan an urgent slide. Insert hotels - Switch to the Acquire workflow step. - Select the Manual and Basic tab. - Select Advanced and the Autoloader tab. 24
- Click on the Access button of the desired face. The selected face is now moved to the loading position and the message box is displayed. Now you can open the door of the autoloader. The following message will be displayed: - Close the door of the autoloader and access the next face. Insert the hotels as described above. Select 1 hotel Switch to the Acquire workflow step. Select Advanced and the Autoloader tab. 25
If necessary, select the Batch Mode button in the Interactive Mode window to activate the Batch Mode. For the hotel you want to scan, click on Confirm or drag and drop. The hotel is displayed in the Interactive Mode window. In case of batch mode interruption, you get the message Do you want to finish scanning this slide or interrupt now? Choose Finish to interrupt the scanning after the current slide has been completed. In this case the scanner completes the scanning of the current slide. After that, the carrier is moved back to the hotel, the batch queue becomes inactive and the Interactive Mode window becomes active. The active scanning face (face in progress) of the batch mode remains inactive. If you switch back to the batch mode later on, the next slide of this slide carrier of the active hotel will be scanned automatically. Choose Interrupt to interrupt the scanning of the active scan at once. In this case the scanner immediately pauses the scanning procedure and moves the carrier back to the hotel. The batch queue becomes inactive and the Interactive Mode window becomes active. The active scanning face (face in progress) of the batch mode remains inactive. If you switch back to the batch mode later on, the scanning of the interrupted slide will be restarted from beginning on automatically. Choose Cancel: In this case the scanner will continue scanning in batch mode. To select individual carriers, click on the Interactive Mode window with the right-hand mouse key. Select Disable All. 26
Select the carriers to be scanned with the left-hand mouse key. Overview Select Scan to have overview images. (The circle at the Scan button turns red.) Select scanning protocols After the first four overviews are finished, they appear automatically (in Manual tab ). You can now define scan protocols for each overview scan. 27
You can change scanning parameters (scan area, z-stack, ) by clicking on the Edit key. The scanning area can either be defined automatically (Use suggested area) or manually with the tool bar on the right part of the screen. When defined, assign the scanning protocol to each slide. Change slide names With the right-hand mouse key on the overview thumbnail, choose Rename and enter the desired name. 28
Scan To scan 1 slide: press the Scan button. To scan several slides: select the slides to scan using the shift key and select Multi scan. The progress of the scan will be indicated as follow: File Export Select in the database list one or more image collections (with the shift key) for export. With the right-hand mouse key, choose Start File Export and the Export Type SCN and confirm with Yes. The selected image collections for File Export (either auto or manual) will show different status during process: Export requested, Exporting, ExportedOK. 29
Eject the slides. Click on Eject. Click on the Access button of the desired face to open the door. Shutdown the scanner if you are the last user See last page Close Leica SCN400 Client Log OFF 30
Switch OFF Switch to the Setup workflow step and click on Shutdown (to shutdown the scanner). Shutdown the PC (or log OFF). 31
Possible states: Busy Idle Disconnected Offline Unknown or unrecoverable error The scanner is working. The scanner is waiting for a task. The scanner is not connected. The scanner is switched off. If the service tool is started, the scanner can not be operated from the Leica SCN400 software. In the application the state will be offline. Unknown state of the scanner. Restart hardware or/and software. Possible status of hotels and carriers: Black with white frame Grey with red frame White Red with white frame Yellow Grey with white frame Carrier waiting for scan Carrier in progress Completed carrier Carrier with failed scans No carrier Carrier disabled Hotel with carriers waiting for scan: Hotel with disabled carriers: Hotel in progress, two carriers completed: Hotel with failed scans: Hotel without carriers: 32