Scanning electron microscopy

Tescan Mira 3

Acquired 2014

How-tos

Access the bigdata server
Description

Avoid the use of USB sticks and external HD (they are usually a liability as they can import viruses). Better, faster and more reliable is to copy your data directly to the UniFr server (Personal Exchange folder, Group folder, Bigdata, personal folder)

Remedy

Map the required network drive

Time requirement

About 30 seconds

Difficulty

Easy

Protocol

Map the BigData network

A the bottom left of your screen, in the Search box, Type ‘This PC‘.

The start menu opens. In the options on the right, click ‘Map network drive‘.

The map network drive utility opens.

Drive Y: (leave unchanged)

Folder \\bigdata.unifr.ch\science\$DEPARTMENT

Uncheck Reconnect at sign-in

Check Connect using different credentials

Fill in the variable $DEPARTMENT according to the affiliation list below

$DEPARTMENT

Department Folder

AMI AMI

Biology Biol

Chemistry Chem

Physics Physics

Medcine Med

Geosciences Geoscience

Example of a folder for an AMI user:

\\bigdata.unifr.ch\science\AMI

Click ‘Finish’

Enter your credentials

Next, a dialog box will pop-up, asking for your credentials.

Username: UNIFR\your Unifr username. See an example below. Do not forget the UNIFR\ before your username!

Password: your UniFr password

Do not check “remember my credentials”

Click OK

System is connecting to BigData

This should not take longer than a few seconds

Disconnecting your BigData drive

Do not forget to disconnect after use:

Start menu > type ‘This PC’

Select Disconnect network drive

A new window pops up. Select Y: (the bigdata drive)

DO NOT DISCONNECT \\TESCAN6123 (communication with the SEM)

Click OK
The maggot screws / assessing the stage
Description

Maggot screws are the small screws that fix the sample into the stage.

If such screw falls into the mechanism of the stage, it can damage the stage.

Remedy

Tighten the screw after usage. Tighten any loose screws.

Time requirement

Few seconds

Difficulty

Easy

Protocol

Before your session

With the chamber open

Check for all maggot screws. Maggot screws sticking out in positions 4 and 5 (left) and in positions 1, 2, 3, 4 and 5 (right). The vibrations of the motors will further loosen the screws until they fall out.

Use the Allen key to tighten the loose screws

Tighten them to a similar extend as you do when you fix a sample: until you feel a resistance, but do not put extensive force on the little screws.

After your session

After you took out your samples, assure all maggot screws are nicely tightened
Extract data from .EMSA files (EDX data)

EDX spectra are typically saves as .EMSA files, a text file containing the metadata and the data points of your spectrum. this R script extracts the data points automatically (Courtesy J. Duruz).

Note: this is an R script. You need to run it in R.

EMSA script

Troubleshooting

I see a windows Login screen. How do I proceed?
Description

When arriving at the SEM, you do not find the standard Mira 3 login screen but a windows Login. You can either see the screen where you can choose between users (Tescan logged on or an account involved in EDX connection)

Remedy

Login

Time requirement

About 10 seconds

Difficulty

Easy

Protocol

If necessary, choose the “Tescan logged on” account

Username: Tescan

Password: tescan

(note the use of the capital T in the username but not in the password)

After login, check if the Mira3 software is running:

You see the Mira 3 login screen

It is minimized in the taskbar. Look for this icon and click it

If no such icon is in the taskbar, then start the MiraTC software from the desktop
Correct Stage Position: Z vs WD & Z
Description

The correct setting for WD & Z after calibration of the stage is 30 mm. The correct setting for Z after calbibration is 40 mm.

If this is not the case at the beginning of your session, please correct this according to the algorithm below. The Z value and WD&Z value will be affected when you raise the stage towards the lens during your session.

Remedy

Manual stage calibration

Time requirement

About 1 minute

Difficulty

Easy, but you can potentially severely damage the system! Be cautious.

Protocol

Manual stage calibration

STEP 1: Z is not 40 mm

The Z value should never be actively changed. If Z is not 40 mm at the start of your session:

Press Calibrate

This results in Z=40mm. WD&Z can still be different from 30mm. See below

STEP 2: Z=40mm, but WD&Z < 30 mm

Select the value in WD&Z and type in 30. This changes WD&Z to 30, but Z will increase equally.

Wait for the stage to finish its movement.

Press Calibrate

STEP 3:

Z=40mm, but WD&Z > 30 mm and < 40mm

Proceed carefully!

Calculate the difference between the WD&Z value and 30. For example, if WD&Z is 38.750mm, then the difference is 8.750.

Add this to the Z value (in this example: Z is changed to 48.750).

Press enter and wait for the stage to finish its movement. This is the only time you are allowed to actively change Z!

Press Home.

STEP 4: Z=40mm, but WD&Z > 40 mm

The maximum range of the stage is 50 mm. If WD&Z > 40 mm, you will need to run the above process iteratively. For example WD&Z=45.

First step: Change Z=50, press enter.

Wait for the stage to finish its movement.

Then: press Home. The result is a WD&Z=35 and a Z=40:

Second step: lower Z: add 5 to to setting of 40 mm to reach 45 mm (because WD&Z is 5 above the intended 30 mm).

Press enter.

Wait for the stage to finish its movement.

Then press Home
The Self test throws an error: No answer from vacuum unit
Description

After login, a self test is being performed. Occationally we witnessed this self test failing at the vacuum unit:

Remedy

restart the Mira software

Time requirement

About 1 minute

Difficulty

Easy

Protocol

Logout of the Mira workspace

Once you see the Mira login / opening screen, close the software by clicking the red X at the top right

Wait 5 seconds

Start the Mira software by doubleclicking the icon on the desktop

The startup will take about 30 seconds:

login as you do normally
Stage rotation misalignment
Description

The position of that stage (1-7) is not matching the actual position in the chamber.

Remedy

Stage calibration

Time requirement

About 1 minute

Difficulty

Easy

Protocol

Stage calibration

In the stage calibration window, below “Home”, find the calibration button

Click the Calibration button

In the chamber view, you can follow the stage going to its point of origin (lowest X, Y and Z) and make a complete stage rotation.

Now the alignment is correct again.
RTP pump error
Description

The software throws an error during pumping: RTP pump error. The pump stops pumping.

Remedy

Click “pump” again

Time requirement

seconds

Difficulty

Easy

Protocol

If this happens once, just click pump again. The issue is due to an overeager temperature sensor in the pump.

If clicking “pump” does not remedy the situation and again throws the same error again and again, there is more at hand. In this case stop your session and inform the admin immediately through OpenIris.
Cannot focus at low HV (< 4 kV)
Description

Focussing and in particular beam centering is not possible at low HV, usually less than 4 kV.

Remedy

Load the default configuration

Time requirement

About 1 minute

Difficulty

Easy

Protocol

Load the default configuration

In the top menu click Options > Configurations > Load

Move to the folder “C:\Tescan\Mira\”

In this folder, find the folder “Configurations”

Choose “defaultOriginal.cfg” (of 05.06.2018)

Adjust the default to low HV

The system will reload the configuration, changing HV to 20 kV and beam intensity to 10.

Set the HV to a low values (e.g. 2 kV)

Set the beam intensity to 7

zoom out and redo the beam centering

focus and stigmation might be quite off. Repeat them as well.