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User Manual

Using This User Manual

To find what you are looking for, use the search function of your browser. You can also navigate the content by tapping the floating navigation icons on the left. 


Information about new features after a software update can be found in the Release Notes document in the katana software folder.


The illustrations provided in this document are for demonstration purposes only. The actual system and information displayed on the software may appear slightly different.

All specifications and descriptions contained in this document are verified to be accurate at the time of printing. However, because continuous improvement is a goal at ConnectomX, we reserve the right to make product modifications at any time. To communicate any inaccuracies or omissions in this document, please send an email to:

2024 ConnectomX Ltd

All information in this document and all microtome software is subject to copyright and other intellectual property rights of ConnectomX Ltd. This material may not be modified, reproduced or copied, in whole or in part, without the prior written permission of ConnectomX Ltd. 

Using This Use Manual



User Manual - Work In



1. USB Connection Status: This display the current connection status to your PC. If it is disconnected, check USB connection and microtome controller power. Click this button to establish connection.

2. RETURN - Knife returns to the fully retracted position.

3.UP - Stage moves up by the set step size. Tap on the number to change step size.

4.DOWN - Stage moves down by the set step size. Tap on the number to change step size.

5.STAR - highlights most recent Z movement log.

6.Max Z lock - Toggle to set the maximum Z of the stage. A red number will appear to show the locked position. The locked position will increase accordingly when slicing in AUTO MODE.

7.FIND ZERO - Stage moves to the lowest position and resets Z to zero.

8.      STAGE POSITION - Current Z position. Tap to set the position manually between 0 and 1300 µm.

9.       KNIFE POSITION - Drag to move the knife. Tap to enable/disable dragging.

10.CUT STOP - Set the end of the cutting window.

11.CUT START - Set the beginning of the cutting window.

12.Auto Settings – Section to change settings for repeated automatic cuts. Switch to approach mode or change  the cut thickness,  the speed that knife travels within the cutting window and number of cuts.

13.ADVANCED SETTINGS - Click to open up some advanced options.

14.AUTO START - Click to begin the automatic cutting.

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