GI - User contributions [en]

JEOL2100 TEM

2026-04-01T13:05:04Z

Hetty: HTreactivate script

The JEOL2100 TEM is a transmission electron microscope within the [[General Instrumentation Department]]. It is generally operated at 200 kV. This microscope is especially suited for:

* Cryo-EM
* Tomography
* High-resolution imaging

== User manuals ==
* [[Media:JEOL2100 HT-start quickguide.pdf|JEOL2100 - HT start guide]], which is a detailed step-by-step guide on how to set the HT to 200 kV.
* [[Media:Userguide HTreactivate script.pdf|JEOL2100 - Userguide HTreactivate script]], which describes how to use the HTreactivate script to automatically restart the HT after an ACD bake-out.

== Current status ==
The current status of the microscope can be found [[Current microscope status#Electron microscopes and sample prep equipment|here]] and on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-electron-microscopy booking website].

== How to get access to this microscope ==
Before using the TEM you have to:

* Complete the introduction training by Hetty. Training is only available for people who are experienced in using the [[JEOL1400 TEM|JEOL1400]].
** Contact Hetty to plan the training
* Book the TEM on the bookings website
** You can only book the TEM after completing the training.

== Technical information ==

* Jeol JEM-2100
* Detectors and camera’s:
** Side mount camera: Gatan 830 Orius SC200, 2048x2048 pixels
** Bottom mount camera: Gatan 895 ultrascan 4000, 4080 x 4080 pixels
** ''STEM detector: JEOL EM-24511 SIOD - currently under repair''
** Dark field detector: JEOL EM-24560
** Gatan Digiscan 2
** ''Bruker Quantax EDS detector large area silicon drift detector (60mm2 ) for energy dispersive spectroscopy - currently broken - unclear if fixable''

File:Userguide HTreactivate script.pdf

2026-04-01T13:02:22Z

Hetty: HTreactivate script userguide JEOL2100 HT restart

== Summary ==
HTreactivate script userguide JEOL2100 HT restart

JEOL2100 TEM

2026-03-27T12:30:33Z

Hetty: added HT start guide

The JEOL2100 TEM is a transmission electron microscope within the [[General Instrumentation Department]]. It is generally operated at 200 kV. This microscope is especially suited for:

* Cryo-EM
* Tomography
* High-resolution imaging

== User manuals ==
* [[Media:JEOL2100 HT-start quickguide.pdf|JEOL2100 HT start guide]], which is a detailed step-by-step guide on how to set the HT to 200 kV.

== Current status ==
The current status of the microscope can be found [[Current microscope status#Electron microscopes and sample prep equipment|here]] and on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-electron-microscopy booking website].

== How to get access to this microscope ==
Before using the TEM you have to:

* Complete the introduction training by Hetty. Training is only available for people who are experienced in using the [[JEOL1400 TEM|JEOL1400]].
** Contact Hetty to plan the training
* Book the TEM on the bookings website
** You can only book the TEM after completing the training.

== Technical information ==

* Jeol JEM-2100
* Detectors and camera’s:
** Side mount camera: Gatan 830 Orius SC200, 2048x2048 pixels
** Bottom mount camera: Gatan 895 ultrascan 4000, 4080 x 4080 pixels
** ''STEM detector: JEOL EM-24511 SIOD - currently under repair''
** Dark field detector: JEOL EM-24560
** Gatan Digiscan 2
** ''Bruker Quantax EDS detector large area silicon drift detector (60mm2 ) for energy dispersive spectroscopy - currently broken - unclear if fixable''

File:JEOL2100 HT-start quickguide.pdf

2026-03-27T12:27:43Z

Hetty: JEOL2100 HT guide start

== Summary ==
JEOL2100 HT guide start

Current microscope status

2026-03-11T10:09:32Z

Hetty: /* Electron microscopes and sample prep equipment */ 2100 status

=== Light microscopes ===
{| class="wikitable"
|+
!Microscope
!Status
!Notes
!Date
|-
|[[Leica SP8X|SP8X]]
|OK
|
|
|-
|[[Leica SP8 Liachroic|SP8-Lia]]
|OK
|488 laser functional again
|20.11.2025
|-
|[[Leica Thunder|Thunder]]
|OK
|
|
|-
|[[Leica Timelapse|Timelapse]]
|OK
|New camera installed
|25.09.2025
|-
|[[PhaseView light sheet|Lightsheet]]
|
|Microscope fully functional, use 4TB SSD drive to take images
|20.11.2025
|-
|[[DM2500]]
|OK
|
|
|-
|[[Nikon sora|SoRa]]
|OK
|
|
|-
|[[Nikon TIRF widefield|TIRF]]
|OK
|
|
|-
|Spinoza server
|OK
|
|
|}

=== Electron microscopes and sample prep equipment ===
{| class="wikitable"
|+
!Machine
!Status
!Notes
!Date
|-
|[[JEOL1400 TEM|JEOL1400]]
|OK
|
|
|-
|[[JEOL2100 TEM|JEOL2100]]
|OK
|HT repaired feb 24-26

|11.03.2026
|-
|
|
|STEM detector broken - under repair
EDX detector broken
|aug 2024
pre 2023
|-
|[[Cryo-holder, cryo-dock and cryo-pumping station|Cryo-dock/station/holder]]
|OK
|
|
|-
|[[HPM100]]
|OK
|
|
|-
|[[EMPACT|EMpact]]
|Broken
|Unsure if can be fixed
|01.09.2025
|-
|[[Vitrobot]]
|OK
|
|
|-
|[[UC-E microtome]]
|OK
|
|
|-
|UC7/FC7 cryo-microtome
|OK
|
|
|-
|[[CCU-010]]
|OK
|
|
|-
|Edward306
|Broken
|Under repair
|
|-
|BAF400
|OK
|
|
|-
|Vibratome
|OK
|
|
|-
|CPD-020
|In storage
|
|
|-
|JFD-030
|OK
|
|
|}

JEOL1400 TEM

2026-02-19T12:35:10Z

Hetty: added slow camera troubleshooter

The JEOL1400 TEM is a [https://en.wikipedia.org/wiki/Transmission_electron_microscopy transmission electron microscope] within the [[General Instrumentation Department]]. It is relatively user-friendly.

[[File:JEOL1400 TEM IMG 8753.JPG|thumb|JEOL1400 TEM]]

== User manuals ==
Please refer to the following documentation:

==== JEOL1400 user guide ====
* [[Media:User guide JEOL1400 HM v1 06a.pdf|JEOL1400 user guide]], which is a detailed step-by-step user guide.

==== Trouble shooters ====
* [[Media:Troubleshooter JEOL1400 no beam.pdf|"No beam" troubleshooter]]. To use when you have trouble obtaining a beam.
* [[Media:JEOL1400 histogram viewer.pdf|"Histogram" troubleshooter]]. Tips on how to adjust the histogram in the JEOL1400 software. Use this when the image on the camera looks weird.
* [[Media:JEOL1400 adjusting the BIAS.pdf|Handout on how to adjust the BIAS.]] Use this when you get the error "beam might not be emitted".
* [[Media:JEOL1400 troubleshooter camera slow.pdf|"Slow camera" troubleshooter]]. To use when the image itself is fine but the camera image is very slow.

==== Advanced user guides ====
These should only be used after receiving training from Hetty.

* [[Media:JEOL1400 ACD.pdf|JEOL1400 ACD user guide]]. How to use the ACD (useful for longer imaging sessions).

*[[Quartet holder]]

== Current status ==
The current status of the microscope can be found [[Current microscope status#Electron microscopes and sample prep equipment|here]] and on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-electron-microscopy booking website].

== How to get access to this microscope ==
Before using the TEM you have to:

* Complete the introduction training by Hetty
** The training takes about 3 hours and is very hands-on.
** Contact Hetty to plan the training
* Book the TEM on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-electron-microscopy bookings website]
** You can only book the TEM after completing the training.

== Technical information ==
* Jeol JEM-1400Flash
* Generally operated at 120 kV
* Filament: [https://en.wikipedia.org/wiki/Lanthanum_hexaboride#Electron_Sources LaB6] crystal
* Camera: Matataki Flash sCMOS

== See also ==

* [[Quartet holder]]

File:JEOL1400 troubleshooter camera slow.pdf

2026-02-19T12:31:10Z

Hetty: JEOL1400 troubeshooter camera slow

== Summary ==
JEOL1400 troubeshooter camera slow

JEOL1400 TEM

2026-02-19T12:29:37Z

Hetty: link to quartet holder page

The JEOL1400 TEM is a [https://en.wikipedia.org/wiki/Transmission_electron_microscopy transmission electron microscope] within the [[General Instrumentation Department]]. It is relatively user-friendly.

[[File:JEOL1400 TEM IMG 8753.JPG|thumb|JEOL1400 TEM]]

== User manuals ==
Please refer to the following documentation:

==== JEOL1400 user guide ====
* [[Media:User guide JEOL1400 HM v1 06a.pdf|JEOL1400 user guide]], which is a detailed step-by-step user guide.

==== Trouble shooters ====
* [[Media:Troubleshooter JEOL1400 no beam.pdf|"No beam" troubleshooter]], to use when you have trouble obtaining a beam.
* [[Media:JEOL1400 histogram viewer.pdf|"Histogram" troubleshooter]]. Tips on how to adjust the histogram in the JEOL1400 software. Use this when the image on the camera looks weird.
* [[Media:JEOL1400 adjusting the BIAS.pdf|Handout on how to adjust the BIAS.]]

==== Advanced user guides ====
These should only be used after receiving training from Hetty.

* [[Media:JEOL1400 ACD.pdf|JEOL1400 ACD user guide]]. How to use the ACD (useful for longer imaging sessions).

*[[Quartet holder]]

== Current status ==
The current status of the microscope can be found [[Current microscope status#Electron microscopes and sample prep equipment|here]] and on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-electron-microscopy booking website].

== How to get access to this microscope ==
Before using the TEM you have to:

* Complete the introduction training by Hetty
** The training takes about 3 hours and is very hands-on.
** Contact Hetty to plan the training
* Book the TEM on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-electron-microscopy bookings website]
** You can only book the TEM after completing the training.

== Technical information ==
* Jeol JEM-1400Flash
* Generally operated at 120 kV
* Filament: [https://en.wikipedia.org/wiki/Lanthanum_hexaboride#Electron_Sources LaB6] crystal
* Camera: Matataki Flash sCMOS

== See also ==

* [[Quartet holder]]

JEOL1400 TEM

2026-02-19T12:28:22Z

Hetty: ACD

The JEOL1400 TEM is a [https://en.wikipedia.org/wiki/Transmission_electron_microscopy transmission electron microscope] within the [[General Instrumentation Department]]. It is relatively user-friendly.

[[File:JEOL1400 TEM IMG 8753.JPG|thumb|JEOL1400 TEM]]

== User manuals ==
Please refer to the following documentation:

==== JEOL1400 user guide ====
* [[Media:User guide JEOL1400 HM v1 06a.pdf|JEOL1400 user guide]], which is a detailed step-by-step user guide.

==== Trouble shooters ====
* [[Media:Troubleshooter JEOL1400 no beam.pdf|"No beam" troubleshooter]], to use when you have trouble obtaining a beam.
* [[Media:JEOL1400 histogram viewer.pdf|"Histogram" troubleshooter]]. Tips on how to adjust the histogram in the JEOL1400 software. Use this when the image on the camera looks weird.
* [[Media:JEOL1400 adjusting the BIAS.pdf|Handout on how to adjust the BIAS.]]

==== Advanced user guides ====
These should only be used after receiving training from Hetty.

* [[Media:JEOL1400 ACD.pdf|JEOL1400 ACD user guide]]. How to use the ACD (useful for longer imaging sessions).

*

== Current status ==
The current status of the microscope can be found [[Current microscope status#Electron microscopes and sample prep equipment|here]] and on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-electron-microscopy booking website].

== How to get access to this microscope ==
Before using the TEM you have to:

* Complete the introduction training by Hetty
** The training takes about 3 hours and is very hands-on.
** Contact Hetty to plan the training
* Book the TEM on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-electron-microscopy bookings website]
** You can only book the TEM after completing the training.

== Technical information ==
* Jeol JEM-1400Flash
* Generally operated at 120 kV
* Filament: [https://en.wikipedia.org/wiki/Lanthanum_hexaboride#Electron_Sources LaB6] crystal
* Camera: Matataki Flash sCMOS

== See also ==

* [[Quartet holder]]

File:JEOL1400 ACD.pdf

2026-02-19T12:26:35Z

Hetty: JEOL1400 ACD anticontamination device user guide

== Summary ==
JEOL1400 ACD anticontamination device user guide

JEOL1400 TEM

2026-02-19T12:25:31Z

Hetty: /* User manuals */ extra user guides etc

The JEOL1400 TEM is a [https://en.wikipedia.org/wiki/Transmission_electron_microscopy transmission electron microscope] within the [[General Instrumentation Department]]. It is relatively user-friendly.

[[File:JEOL1400 TEM IMG 8753.JPG|thumb|JEOL1400 TEM]]

== User manuals ==
Please refer to the following documentation:

==== JEOL1400 user guide ====
* [[Media:User guide JEOL1400 HM v1 06a.pdf|JEOL1400 user guide]], which is a detailed step-by-step user guide.

==== Trouble shooters ====
* [[Media:Troubleshooter JEOL1400 no beam.pdf|"No beam" troubleshooter]], to use when you have trouble obtaining a beam.
* [[Media:JEOL1400 histogram viewer.pdf|"Histogram" troubleshooter]]. Tips on how to adjust the histogram in the JEOL1400 software. Use this when the image on the camera looks weird.
* [[Media:JEOL1400 adjusting the BIAS.pdf|Handout on how to adjust the BIAS.]]

==== Advanced user guides ====
These should only be used after receiving training from Hetty.

*

== Current status ==
The current status of the microscope can be found [[Current microscope status#Electron microscopes and sample prep equipment|here]] and on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-electron-microscopy booking website].

== How to get access to this microscope ==
Before using the TEM you have to:

* Complete the introduction training by Hetty
** The training takes about 3 hours and is very hands-on.
** Contact Hetty to plan the training
* Book the TEM on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-electron-microscopy bookings website]
** You can only book the TEM after completing the training.

== Technical information ==
* Jeol JEM-1400Flash
* Generally operated at 120 kV
* Filament: [https://en.wikipedia.org/wiki/Lanthanum_hexaboride#Electron_Sources LaB6] crystal
* Camera: Matataki Flash sCMOS

== See also ==

* [[Quartet holder]]

Current microscope status

2026-02-13T13:57:36Z

Hetty: Update 2100 status

=== Light microscopes ===
{| class="wikitable"
|+
!Microscope
!Status
!Notes
!Date
|-
|[[Leica SP8X|SP8X]]
|OK
|
|
|-
|[[Leica SP8 Liachroic|SP8-Lia]]
|OK
|488 laser functional again
|20.11.2025
|-
|[[Leica Thunder|Thunder]]
|OK
|
|
|-
|[[Leica Timelapse|Timelapse]]
|OK
|New camera installed
|25.09.2025
|-
|[[PhaseView light sheet|Lightsheet]]
|
|Microscope fully functional, use 4TB SSD drive to take images
|20.11.2025
|-
|[[DM2500]]
|OK
|
|
|-
|[[Nikon sora|SoRa]]
|OK
|
|
|-
|[[Nikon TIRF widefield|TIRF]]
|OK
|
|
|-
|Spinoza server
|OK
|
|
|}

=== Electron microscopes and sample prep equipment ===
{| class="wikitable"
|+
!Machine
!Status
!Notes
!Date
|-
|[[JEOL1400 TEM|JEOL1400]]
|OK
|
|
|-
|[[JEOL2100 TEM|JEOL2100]]
|Broken
|HT problems. Contacted JEOL.
Repair is planned for Feb 24-26

|12.11.2025
13.02.2026
|-
|
|
|STEM detector broken - under repair
EDX detector broken
|aug 2024
pre 2023
|-
|[[Cryo-holder, cryo-dock and cryo-pumping station|Cryo-dock/station/holder]]
|OK
|
|
|-
|[[HPM100]]
|OK
|
|
|-
|[[EMPACT|EMpact]]
|Broken
|Unsure if can be fixed
|01.09.2025
|-
|[[Vitrobot]]
|OK
|
|
|-
|[[UC-E microtome]]
|OK
|
|
|-
|UC7/FC7 cryo-microtome
|OK
|
|
|-
|[[CCU-010]]
|OK
|
|
|-
|Edward306
|Broken
|Under repair
|
|-
|BAF400
|OK
|
|
|-
|Vibratome
|OK
|
|
|-
|CPD-020
|In storage
|
|
|-
|JFD-030
|OK
|
|
|}

Current microscope status

2026-01-16T10:12:28Z

Hetty: /* Electron microscopes and sample prep equipment */

=== Light microscopes ===
{| class="wikitable"
|+
!Microscope
!Status
!Notes
!Date
|-
|[[Leica SP8X|SP8X]]
|OK
|
|
|-
|[[Leica SP8 Liachroic|SP8-Lia]]
|OK
|488 laser functional again
|20.11.2025
|-
|[[Leica Thunder|Thunder]]
|OK
|
|
|-
|[[Leica Timelapse|Timelapse]]
|OK
|New camera installed
|25.09.2025
|-
|[[PhaseView light sheet|Lightsheet]]
|
|Microscope fully functional, use 4TB SSD drive to take images
|20.11.2025
|-
|[[DM2500]]
|OK
|
|
|-
|[[Nikon sora|SoRa]]
|OK
|
|
|-
|[[Nikon TIRF widefield|TIRF]]
|OK
|
|
|-
|Spinoza server
|OK
|
|
|}

=== Electron microscopes and sample prep equipment ===
{| class="wikitable"
|+
!Machine
!Status
!Notes
!Date
|-
|[[JEOL1400 TEM|JEOL1400]]
|OK
|
|
|-
|[[JEOL2100 TEM|JEOL2100]]
|Broken
|HT problems. Contacted JEOL.
Repair is being arranged.

|12.11.2025
16.01.2026
|-
|
|
|STEM detector broken - under repair
EDX detector broken
|aug 2024
pre 2023
|-
|[[Cryo-holder, cryo-dock and cryo-pumping station|Cryo-dock/station/holder]]
|OK
|
|
|-
|[[HPM100]]
|OK
|
|
|-
|[[EMPACT|EMpact]]
|Broken
|Unsure if can be fixed
|01.09.2025
|-
|[[Vitrobot]]
|OK
|
|
|-
|[[UC-E microtome]]
|OK
|
|
|-
|UC7/FC7 cryo-microtome
|OK
|
|
|-
|[[CCU-010]]
|OK
|
|
|-
|Edward306
|Broken
|Under repair
|
|-
|BAF400
|OK
|
|
|-
|Vibratome
|OK
|
|
|-
|CPD-020
|In storage
|
|
|-
|JFD-030
|OK
|
|
|}

Current microscope status

2026-01-16T10:11:28Z

Hetty: /* Department closure during the Christmas holiday (update 14.11) */

=== Light microscopes ===
{| class="wikitable"
|+
!Microscope
!Status
!Notes
!Date
|-
|[[Leica SP8X|SP8X]]
|OK
|
|
|-
|[[Leica SP8 Liachroic|SP8-Lia]]
|OK
|488 laser functional again
|20.11.2025
|-
|[[Leica Thunder|Thunder]]
|OK
|
|
|-
|[[Leica Timelapse|Timelapse]]
|OK
|New camera installed
|25.09.2025
|-
|[[PhaseView light sheet|Lightsheet]]
|
|Microscope fully functional, use 4TB SSD drive to take images
|20.11.2025
|-
|[[DM2500]]
|OK
|
|
|-
|[[Nikon sora|SoRa]]
|OK
|
|
|-
|[[Nikon TIRF widefield|TIRF]]
|OK
|
|
|-
|Spinoza server
|OK
|
|
|}

=== Electron microscopes and sample prep equipment ===
{| class="wikitable"
|+
!Machine
!Status
!Notes
!Date
|-
|[[JEOL1400 TEM|JEOL1400]]
|OK
|
|
|-
|[[JEOL2100 TEM|JEOL2100]]
|Broken
|HT problems. Contacted JEOL.
JEOL technician visit planned for 05.12

|12.11.2025
26.11.2025
|-
|
|
|STEM detector broken - under repair
EDX detector broken
|aug 2024
pre 2023
|-
|[[Cryo-holder, cryo-dock and cryo-pumping station|Cryo-dock/station/holder]]
|OK
|
|
|-
|[[HPM100]]
|OK
|
|
|-
|[[EMPACT|EMpact]]
|Broken
|Unsure if can be fixed
|01.09.2025
|-
|[[Vitrobot]]
|OK
|
|
|-
|[[UC-E microtome]]
|OK
|
|
|-
|UC7/FC7 cryo-microtome
|OK
|
|
|-
|[[CCU-010]]
|OK
|
|
|-
|Edward306
|Broken
|Under repair
|
|-
|BAF400
|OK
|
|
|-
|Vibratome
|OK
|
|
|-
|CPD-020
|In storage
|
|
|-
|JFD-030
|OK
|
|
|}

Current microscope status

2025-11-27T10:58:41Z

Hetty:

==== Department closure during the Christmas holiday (update 14.11) ====

* The Huygens building and therefor the GI department will be closed during the Christmas holiday from Monday 22 December up to and including January 2nd.
** Only people with special card access can enter the GI department. Remember to use the overwork timer!
** No support staff will be on site.
** Access to liquid nitrogen is not guaranteed.
* On January 5-6-7 the Huygens building will inaccessible due to maintenance work. No one will be allowed inside; this includes people with extra card access.

=== Light microscopes ===
{| class="wikitable"
|+
!Microscope
!Status
!Notes
!Date
|-
|[[Leica SP8X|SP8X]]
|OK
|
|
|-
|[[Leica SP8 Liachroic|SP8-Lia]]
|OK
|488 laser functional again
|20.11.2025
|-
|[[Leica Thunder|Thunder]]
|OK
|
|
|-
|[[Leica Timelapse|Timelapse]]
|OK
|New camera installed
|25.09.2025
|-
|[[PhaseView light sheet|Lightsheet]]
|
|Microscope fully functional, use 4TB SSD drive to take images
|20.11.2025
|-
|[[DM2500]]
|OK
|
|
|-
|[[Nikon sora|SoRa]]
|OK
|
|
|-
|[[Nikon TIRF widefield|TIRF]]
|OK
|
|
|-
|Spinoza server
|OK
|
|
|}

=== Electron microscopes and sample prep equipment ===
{| class="wikitable"
|+
!Machine
!Status
!Notes
!Date
|-
|[[JEOL1400 TEM|JEOL1400]]
|OK
|
|
|-
|[[JEOL2100 TEM|JEOL2100]]
|Broken
|HT problems. Contacted JEOL.
JEOL technician visit planned for 05.12

|12.11.2025
26.11.2025
|-
|
|
|STEM detector broken - under repair
EDX detector broken
|aug 2024
pre 2023
|-
|[[Cryo-holder, cryo-dock and cryo-pumping station|Cryo-dock/station/holder]]
|OK
|
|
|-
|[[HPM100]]
|OK
|
|
|-
|[[EMPACT|EMpact]]
|Broken
|Unsure if can be fixed
|01.09.2025
|-
|[[Vitrobot]]
|OK
|
|
|-
|[[UC-E microtome]]
|OK
|
|
|-
|UC7/FC7 cryo-microtome
|OK
|
|
|-
|[[CCU-010]]
|OK
|
|
|-
|Edward306
|Broken
|Under repair
|
|-
|BAF400
|OK
|
|
|-
|Vibratome
|OK
|
|
|-
|CPD-020
|In storage
|
|
|-
|JFD-030
|OK
|
|
|}

Quartet holder

2025-11-24T12:49:45Z

Hetty:

The quartet holder (EM-01070 SQH) is a TEM sample holder that can be used on the [[JEOL1400 TEM|JEOL1400]]. It can hold up to three grids at the same time, speeding up data aquisition. Before using this holder you have to complete the quartet holder training (~30 min, ask Hetty).

=== Documentation ===

*[[Media:Protocol quartet holder.pdf| Quartet holder user guide]]

JEOL1400 TEM

2025-11-24T12:49:06Z

Hetty:

The JEOL1400 TEM is a [https://en.wikipedia.org/wiki/Transmission_electron_microscopy transmission electron microscope] within the [[General Instrumentation Department]]. It is relatively user-friendly.

[[File:JEOL1400 TEM IMG 8753.JPG|thumb|JEOL1400 TEM]]

== User manuals ==
Please refer to the following documentation:

* [[Media:User guide JEOL1400 HM v1 06a.pdf|JEOL1400 user guide]], which is a detailed step-by-step user guide.
* [[Media:Troubleshooter JEOL1400 no beam.pdf|"No beam" troubleshooter]], to use when you have trouble obtaining a beam.
* [[Media:JEOL1400 histogram viewer.pdf|"Histogram" troubleshooter]]. Tips on how to adjust the histogram in the JEOL1400 software. Use this when the image on the camera looks weird.
* [[Media:JEOL1400 adjusting the BIAS.pdf|Handout on how to adjust the BIAS.]]

== Current status ==
The current status of the microscope can be found [[Current microscope status#Electron microscopes and sample prep equipment|here]] and on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-electron-microscopy booking website].

== How to get access to this microscope ==
Before using the TEM you have to:

* Complete the introduction training by Hetty
** The training takes about 3 hours and is very hands-on.
** Contact Hetty to plan the training
* Book the TEM on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-electron-microscopy bookings website]
** You can only book the TEM after completing the training.

== Technical information ==
* Jeol JEM-1400Flash
* Generally operated at 120 kV
* Filament: [https://en.wikipedia.org/wiki/Lanthanum_hexaboride#Electron_Sources LaB6] crystal
* Camera: Matataki Flash sCMOS

== See also ==

* [[Quartet holder]]

Quartet holder

2025-11-24T12:44:04Z

Hetty:

The quartet holder (EM-01070 SQH) is a TEM sample holder that can be used on the [[JEOL1400 TEM|JEOL1400]]. It can hold up to three grids at the same time and there can speed up data aquisition. Before using this holder you have to complete the quartet holder training (~30 min, ask Hetty).

=== Documentation ===

*[[Media:Protocol quartet holder.pdf| Quartet holder user guide]]

Quartet holder

2025-11-24T12:43:31Z

Hetty:

The quartet holder (EM-01070 SQH) is a TEM sample holder that can be used on the JEOL1400. It can hold up to three grids at the same time and there can speed up data aquisition. Before using this holder you have to complete the quartet holder training (~30 min, ask Hetty).

=== Documentation ===

*[[media:Protocol quartet holder.pdf | Quartet holder user guide]]

Quartet holder

2025-11-24T12:42:56Z

Hetty:

The quartet holder (EM-01070 SQH) is a TEM sample holder that can be used on the JEOL1400. It can hold up to three grids at the same time and there can speed up data aquisition. Before using this holder you have to complete the quartet holder training (~30 min, ask Hetty).

=== Documentation ===

*[[media: File:Protocol quartet holder.pdf | Quartet holder user guide]]

File:Protocol quartet holder.pdf

2025-11-24T12:41:11Z

Hetty: Protocol quartet holder

== Summary ==
Protocol quartet holder

Quartet holder

2025-11-24T12:40:16Z

Hetty: Started page

Electron microscopy at the GI department

2025-11-24T12:37:07Z

Hetty: Made page for quartet holder

This page lists the options for performing electron microscopy at the GI department.

=== List of equipment ===

==== Electron microscopes ====

* [[JEOL1400 TEM]]
* [[JEOL2100 TEM]]

==== Electron microscope sample holders and cryo-accessories ====

* Quick-change holder (2x)
* [[Quartet holder]]
* Single-tilt holder
* [[Cryo-holder, cryo-dock and cryo-pumping station]]
* Beryllium holder (for EDX)
* Dual axis room temperature tomography holder

==== Sample prep equipment ====

* Safematic [[CCU-010]] coater for glow discharging, carbon coating and sputter coating
* FEI [[Vitrobot]] plungefreezer
* Leica [[HPM100]] high-pressure freezer
* Leica [[EMPACT]] high-pressure freezer
* Reichert-Jung [[UC-E microtome]]
* Leica UC7/FC7 cryo-microtome
* Leica [[AFS1/AFS2]] freeze-substitution machines
* Leica Vibratome VT1000S
* EM KMR2 knife maker
* Balzers BAF400 freeze etcher
* Balzers CPD-020 critical point dryer
* Edwards 306 thermal evaporation coater

Current microscope status

2025-11-21T07:30:10Z

Hetty:

==== Department closure during the Christmas holiday (update 14.11) ====

* The Huygens building and therefor the GI department will be closed during the Christmas holiday from Monday 22 December up to and including January 2nd.
** Only people with special card access can enter the GI department. Remember to use the overwork timer!
** No support staff will be on site.
** Access to liquid nitrogen is not guaranteed.
* On January 5-6-7 the Huygens building will inaccessible due to maintenance work. No one will be allowed inside; this includes people with extra card access.

=== Light microscopes ===
{| class="wikitable"
|+
!Microscope
!Status
!Notes
!Date
|-
|[[Leica SP8X|SP8X]]
|OK
|
|
|-
|[[Leica SP8 Liachroic|SP8-Lia]]
|OK
|488 laser functional again
|20.11.2025
|-
|[[Leica Thunder|Thunder]]
|OK
|
|
|-
|[[Leica Timelapse|Timelapse]]
|OK
|New camera installed
|25.09.2025
|-
|[[PhaseView light sheet|Lightsheet]]
|
|Microscope fully functional, use 4TB SSD drive to take images
|20.11.2025
|-
|[[DM2500]]
|OK
|
|
|-
|[[Nikon sora|SoRa]]
|OK
|
|
|-
|[[Nikon TIRF widefield|TIRF]]
|OK
|
|
|-
|Spinoza server
|OK
|
|
|}

=== Electron microscopes and sample prep equipment ===
{| class="wikitable"
|+
!Machine
!Status
!Notes
!Date
|-
|[[JEOL1400 TEM|JEOL1400]]
|OK
|
|
|-
|[[JEOL2100 TEM|JEOL2100]]
|Broken
|HT problems. Contacted JEOL.
No date as of yet, but will not happen in November

|12.11.2025
14.11.2025
|-
|
|
|STEM detector broken - under repair
EDX detector broken
|aug 2024
pre 2023
|-
|[[Cryo-holder, cryo-dock and cryo-pumping station|Cryo-dock/station/holder]]
|OK
|
|
|-
|[[HPM100]]
|OK
|
|
|-
|[[EMPACT|EMpact]]
|Broken
|Unsure if can be fixed
|01.09.2025
|-
|[[Vitrobot]]
|OK
|
|
|-
|[[UC-E microtome]]
|OK
|
|
|-
|UC7/FC7 cryo-microtome
|OK
|
|
|-
|[[CCU-010]]
|OK
|
|
|-
|Edward306
|Broken
|Under repair
|
|-
|BAF400
|OK
|
|
|-
|Vibratome
|OK
|
|
|-
|CPD-020
|In storage
|
|
|-
|JFD-030
|OK
|
|
|}

JEOL1400 TEM

2025-11-20T15:00:47Z

Hetty: Added BIAS file

The JEOL1400 TEM is a [https://en.wikipedia.org/wiki/Transmission_electron_microscopy transmission electron microscope] within the [[General Instrumentation Department]]. It is relatively user-friendly.

[[File:JEOL1400 TEM IMG 8753.JPG|thumb|JEOL1400 TEM]]

== User manuals ==
Please refer to the following documentation:

* [[Media:User guide JEOL1400 HM v1 06a.pdf|JEOL1400 user guide]], which is a detailed step-by-step user guide.
* [[Media:Troubleshooter JEOL1400 no beam.pdf|"No beam" troubleshooter]], to use when you have trouble obtaining a beam.
* [[Media:JEOL1400 histogram viewer.pdf|"Histogram" troubleshooter]]. Tips on how to adjust the histogram in the JEOL1400 software. Use this when the image on the camera looks weird.
* [[Media:JEOL1400 adjusting the BIAS.pdf|Handout on how to adjust the BIAS.]]

== Current status ==
The current status of the microscope can be found [[Current microscope status#Electron microscopes and sample prep equipment|here]] and on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-electron-microscopy booking website].

== How to get access to this microscope ==
Before using the TEM you have to:

* Complete the introduction training by Hetty
** The training takes about 3 hours and is very hands-on.
** Contact Hetty to plan the training
* Book the TEM on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-electron-microscopy bookings website]
** You can only book the TEM after completing the training.

== Technical information ==
* Jeol JEM-1400Flash
* Generally operated at 120 kV
* Filament: [https://en.wikipedia.org/wiki/Lanthanum_hexaboride#Electron_Sources LaB6] crystal
* Camera: Matataki Flash sCMOS

File:JEOL1400 adjusting the BIAS.pdf

2025-11-20T14:58:38Z

Hetty: JEOL1400 adjusting the BIAS user guide

== Summary ==
JEOL1400 adjusting the BIAS user guide

Current microscope status

2025-11-14T11:41:31Z

Hetty: Kerst update

==== Department closure during the Christmas holiday (update 14.11) ====

* The Huygens building and therefor the GI department will be closed during the Christmas holiday from Monday 22 December up to and including January 2nd.
** Only people with special card access can enter the GI department. Remember to use the overwork timer!
** No support staff will be on site.
** Access to liquid nitrogen is not guaranteed.
* On January 5-6-7 the Huygens building will inaccessible due to maintenance work. No one will be allowed inside; this includes people with extra card access.

=== Light microscopes ===
{| class="wikitable"
|+
!Microscope
!Status
!Notes
!Date
|-
|[[Leica SP8X|SP8X]]
|OK
|
|
|-
|[[Leica SP8 Liachroic|SP8-Lia]]
|OK
|488 laser dodgy - don't turn it off!
|27.08.2025
|-
|[[Leica Thunder|Thunder]]
|OK
|
|
|-
|[[Leica Timelapse|Timelapse]]
|OK
|New camera installed
|25.09.2025
|-
|[[PhaseView light sheet|Lightsheet]]
|
|561 laser weak+ software out of date
Broken parts are sent for repair (PhaseView corp., Paris, France)
|03.10.2025
|-
|[[DM2500]]
|OK
|
|
|-
|[[Nikon sora|SoRa]]
|OK
|
|
|-
|[[Nikon TIRF widefield|TIRF]]
|OK
|
|
|-
|Spinoza server
|OK
|
|
|}

=== Electron microscopes and sample prep equipment ===
{| class="wikitable"
|+
!Machine
!Status
!Notes
!Date
|-
|[[JEOL1400 TEM|JEOL1400]]
|OK
|
|
|-
|[[JEOL2100 TEM|JEOL2100]]
|Broken
|HT problems. Contacted JEOL.
No date as of yet, but will not happen in November

|12.11.2025
14.11.2025
|-
|
|
|STEM detector broken - under repair
EDX detector broken
|aug 2024
pre 2023
|-
|[[Cryo-holder, cryo-dock and cryo-pumping station|Cryo-dock/station/holder]]
|OK
|
|
|-
|[[HPM100]]
|OK
|
|
|-
|[[EMPACT|EMpact]]
|Broken
|Unsure if can be fixed
|01.09.2025
|-
|[[Vitrobot]]
|OK
|
|
|-
|[[UC-E microtome]]
|OK
|
|
|-
|UC7/FC7 cryo-microtome
|OK
|
|
|-
|[[CCU-010]]
|OK
|
|
|-
|Edward306
|Broken
|Under repair
|
|-
|BAF400
|Broken
|Under repair
|
|-
|Vibratome
|OK
|
|
|-
|CPD-020
|In storage
|
|
|-
|JFD-030
|OK
|
|
|}

Current microscope status

2025-11-14T09:58:32Z

Hetty: Update status UC-E

==== Department closure during the Christmas holiday: from 22 Dec 2025 - 7 Jan 2026 ====
The Huygens building and therefor the GI department will be closed during the Christmas holiday from Monday 22 December onwards. Due to maintenance work on the Huygens building, this closure is extended up to including Wednesday January 7th. It is at the moment (03.11.2025) unclear if the microscopes need to be powered off during this time period. No one can the access the GI department during the Christmas closure period; this includes people who have extended access outside of normal opening hours.

=== Light microscopes ===
{| class="wikitable"
|+
!Microscope
!Status
!Notes
!Date
|-
|[[Leica SP8X|SP8X]]
|OK
|
|
|-
|[[Leica SP8 Liachroic|SP8-Lia]]
|OK
|488 laser dodgy - don't turn it off!
|27.08.2025
|-
|[[Leica Thunder|Thunder]]
|OK
|
|
|-
|[[Leica Timelapse|Timelapse]]
|OK
|New camera installed
|25.09.2025
|-
|[[PhaseView light sheet|Lightsheet]]
|
|561 laser weak+ software out of date
Broken parts are sent for repair (PhaseView corp., Paris, France)
|03.10.2025
|-
|[[DM2500]]
|OK
|
|
|-
|[[Nikon sora|SoRa]]
|OK
|
|
|-
|[[Nikon TIRF widefield|TIRF]]
|OK
|
|
|-
|Spinoza server
|OK
|
|
|}

=== Electron microscopes and sample prep equipment ===
{| class="wikitable"
|+
!Machine
!Status
!Notes
!Date
|-
|[[JEOL1400 TEM|JEOL1400]]
|OK
|
|
|-
|[[JEOL2100 TEM|JEOL2100]]
|Broken
|HT problems. Contacted JEOL.
No date as of yet, but will not happen in November

|12.11.2025
14.11.2025
|-
|
|
|STEM detector broken - under repair
EDX detector broken
|aug 2024
pre 2023
|-
|[[Cryo-holder, cryo-dock and cryo-pumping station|Cryo-dock/station/holder]]
|OK
|
|
|-
|[[HPM100]]
|OK
|
|
|-
|[[EMPACT|EMpact]]
|Broken
|Unsure if can be fixed
|01.09.2025
|-
|[[Vitrobot]]
|OK
|
|
|-
|[[UC-E microtome]]
|OK
|
|
|-
|UC7/FC7 cryo-microtome
|OK
|
|
|-
|[[CCU-010]]
|OK
|
|
|-
|Edward306
|Broken
|Under repair
|
|-
|BAF400
|Broken
|Under repair
|
|-
|Vibratome
|OK
|
|
|-
|CPD-020
|In storage
|
|
|-
|JFD-030
|OK
|
|
|}

Current microscope status

2025-11-14T09:57:53Z

Hetty: Update 2100 status

==== Department closure during the Christmas holiday: from 22 Dec 2025 - 7 Jan 2026 ====
The Huygens building and therefor the GI department will be closed during the Christmas holiday from Monday 22 December onwards. Due to maintenance work on the Huygens building, this closure is extended up to including Wednesday January 7th. It is at the moment (03.11.2025) unclear if the microscopes need to be powered off during this time period. No one can the access the GI department during the Christmas closure period; this includes people who have extended access outside of normal opening hours.

=== Light microscopes ===
{| class="wikitable"
|+
!Microscope
!Status
!Notes
!Date
|-
|[[Leica SP8X|SP8X]]
|OK
|
|
|-
|[[Leica SP8 Liachroic|SP8-Lia]]
|OK
|488 laser dodgy - don't turn it off!
|27.08.2025
|-
|[[Leica Thunder|Thunder]]
|OK
|
|
|-
|[[Leica Timelapse|Timelapse]]
|OK
|New camera installed
|25.09.2025
|-
|[[PhaseView light sheet|Lightsheet]]
|
|561 laser weak+ software out of date
Broken parts are sent for repair (PhaseView corp., Paris, France)
|03.10.2025
|-
|[[DM2500]]
|OK
|
|
|-
|[[Nikon sora|SoRa]]
|OK
|
|
|-
|[[Nikon TIRF widefield|TIRF]]
|OK
|
|
|-
|Spinoza server
|OK
|
|
|}

=== Electron microscopes and sample prep equipment ===
{| class="wikitable"
|+
!Machine
!Status
!Notes
!Date
|-
|[[JEOL1400 TEM|JEOL1400]]
|OK
|
|
|-
|[[JEOL2100 TEM|JEOL2100]]
|Broken
|HT problems. Contacted JEOL.
No date as of yet, but will not happen in November

|12.11.2025
14.11.2025
|-
|
|
|STEM detector broken - under repair
EDX detector broken
|aug 2024
pre 2023
|-
|[[Cryo-holder, cryo-dock and cryo-pumping station|Cryo-dock/station/holder]]
|OK
|
|
|-
|[[HPM100]]
|OK
|
|
|-
|[[EMPACT|EMpact]]
|Broken
|Unsure if can be fixed
|01.09.2025
|-
|[[Vitrobot]]
|OK
|
|
|-
|[[UC-E microtome]]
|Broken
|Under repair - contact Hetty if you need it soon
|01.09.2025
|-
|UC7/FC7 cryo-microtome
|OK
|
|
|-
|[[CCU-010]]
|OK
|
|
|-
|Edward306
|Broken
|Under repair
|
|-
|BAF400
|Broken
|Under repair
|
|-
|Vibratome
|OK
|
|
|-
|CPD-020
|In storage
|
|
|-
|JFD-030
|OK
|
|
|}

Current microscope status

2025-11-12T10:04:54Z

Hetty:

==== Department closure during the Christmas holiday: from 22 Dec 2025 - 7 Jan 2026 ====
The Huygens building and therefor the GI department will be closed during the Christmas holiday from Monday 22 December onwards. Due to maintenance work on the Huygens building, this closure is extended up to including Wednesday January 7th. It is at the moment (03.11.2025) unclear if the microscopes need to be powered off during this time period. No one can the access the GI department during the Christmas closure period; this includes people who have extended access outside of normal opening hours.

=== Light microscopes ===
{| class="wikitable"
|+
!Microscope
!Status
!Notes
!Date
|-
|[[Leica SP8X|SP8X]]
|OK
|
|
|-
|[[Leica SP8 Liachroic|SP8-Lia]]
|OK
|488 laser dodgy - don't turn it off!
|27.08.2025
|-
|[[Leica Thunder|Thunder]]
|OK
|
|
|-
|[[Leica Timelapse|Timelapse]]
|OK
|New camera installed
|25.09.2025
|-
|[[PhaseView light sheet|Lightsheet]]
|
|561 laser weak+ software out of date
Broken parts are sent for repair (PhaseView corp., Paris, France)
|03.10.2025
|-
|[[DM2500]]
|OK
|
|
|-
|[[Nikon sora|SoRa]]
|OK
|
|
|-
|[[Nikon TIRF widefield|TIRF]]
|OK
|
|
|-
|Spinoza server
|OK
|
|
|}

=== Electron microscopes and sample prep equipment ===
{| class="wikitable"
|+
!Machine
!Status
!Notes
!Date
|-
|[[JEOL1400 TEM|JEOL1400]]
|OK
|
|
|-
|[[JEOL2100 TEM|JEOL2100]]
|Broken
|HT problems. Contacted JEOL
STEM detector broken - under repair

EDX detector broken
|12.11.2025
aug 2024

pre 2023
|-
|[[Cryo-holder, cryo-dock and cryo-pumping station|Cryo-dock/station/holder]]
|OK
|
|
|-
|[[HPM100]]
|OK
|
|
|-
|[[EMPACT|EMpact]]
|Broken
|Unsure if can be fixed
|01.09.2025
|-
|[[Vitrobot]]
|OK
|
|
|-
|[[UC-E microtome]]
|Broken
|Under repair - contact Hetty if you need it soon
|01.09.2025
|-
|UC7/FC7 cryo-microtome
|OK
|
|
|-
|[[CCU-010]]
|OK
|
|
|-
|Edward306
|Broken
|Under repair
|
|-
|BAF400
|Broken
|Under repair
|
|-
|Vibratome
|OK
|
|
|-
|CPD-020
|In storage
|
|
|-
|JFD-030
|OK
|
|
|}

Current microscope status

2025-11-12T10:04:27Z

Hetty: 2100 status

==== Department closure during the Christmas holiday: from 22 Dec 2025 - 7 Jan 2026 ====
The Huygens building and therefor the GI department will be closed during the Christmas holiday from Monday 22 December onwards. Due to maintenance work on the Huygens building, this closure is extended up to including Wednesday January 7th. It is at the moment (03.11.2025) unclear if the microscopes need to be powered off during this time period. No one can the access the GI department during the Christmas closure period; this includes people who have extended access outside of normal opening hours.

=== Light microscopes ===
{| class="wikitable"
|+
!Microscope
!Status
!Notes
!Date
|-
|[[Leica SP8X|SP8X]]
|OK
|
|
|-
|[[Leica SP8 Liachroic|SP8-Lia]]
|OK
|488 laser dodgy - don't turn it off!
|27.08.2025
|-
|[[Leica Thunder|Thunder]]
|OK
|
|
|-
|[[Leica Timelapse|Timelapse]]
|OK
|New camera installed
|25.09.2025
|-
|[[PhaseView light sheet|Lightsheet]]
|
|561 laser weak+ software out of date
Broken parts are sent for repair (PhaseView corp., Paris, France)
|03.10.2025
|-
|[[DM2500]]
|OK
|
|
|-
|[[Nikon sora|SoRa]]
|OK
|
|
|-
|[[Nikon TIRF widefield|TIRF]]
|OK
|
|
|-
|Spinoza server
|OK
|
|
|}

=== Electron microscopes and sample prep equipment ===
{| class="wikitable"
|+
!Machine
!Status
!Notes
!Date
|-
|[[JEOL1400 TEM|JEOL1400]]
|OK
|
|
|-
|[[JEOL2100 TEM|JEOL2100]]
|Broken
|HT problems. Contacted JEOL
STEM detector broken - under repair
EDX detector broken
|12.11.2025
aug 2024
pre 2023
|-
|[[Cryo-holder, cryo-dock and cryo-pumping station|Cryo-dock/station/holder]]
|OK
|
|
|-
|[[HPM100]]
|OK
|
|
|-
|[[EMPACT|EMpact]]
|Broken
|Unsure if can be fixed
|01.09.2025
|-
|[[Vitrobot]]
|OK
|
|
|-
|[[UC-E microtome]]
|Broken
|Under repair - contact Hetty if you need it soon
|01.09.2025
|-
|UC7/FC7 cryo-microtome
|OK
|
|
|-
|[[CCU-010]]
|OK
|
|
|-
|Edward306
|Broken
|Under repair
|
|-
|BAF400
|Broken
|Under repair
|
|-
|Vibratome
|OK
|
|
|-
|CPD-020
|In storage
|
|
|-
|JFD-030
|OK
|
|
|}

CCU-010

2025-11-06T08:18:17Z

Hetty:

The [https://www.safematic.ch/ Safematic] CCU-010 HV can be used for glow discharging, plasma cleaning, carbon coating and sputter coating of TEM grids and other small objects.

The machine comes with two exchangeable head modules. The black head module is used for carbon-coating and glow discharging/plasma cleaning. The red head module is for sputter coating. We have a 20/80 gold/palladium sputter target.

[[File:CCU010 20250613 104541 kopie.jpg|thumb|Safematic CCU-010. The carbon-coating and glow discharge head module is installed. ]]

== Manuals ==
* [[:File:Protocol glow discharging TEM grids CCU010 250616.pdf|User manual glow discharge of TEM grids]]

== Current status ==
The current status of the microscope can be found [[Current microscope status#Electron microscopes and sample prep equipment|here]] and on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-electron-microscopy booking website].

== Technical specifications ==

* Safematic CCU-010 HV
* SP-010 sputter head
* CT-010 carbon thread evaporation module
* GD-010 glow discharge module
* HS-010 head storage box
* Stages:
** Standard stage
** ST-010 object slide table
** PS-006 planetary gear table
** Rotary support for PS-006

Current microscope status

2025-11-03T09:54:22Z

Hetty: Kerstsluiting

==== Department closure during the Christmas holiday: from 22 Dec 2025 - 7 Jan 2026 ====
The Huygens building and therefor the GI department will be closed during the Christmas holiday from Monday 22 December onwards. Due to maintenance work on the Huygens building, this closure is extended up to including Wednesday January 7th. It is at the moment (03.11.2025) unclear if the microscopes need to be powered off during this time period. No one can the access the GI department during the Christmas closure period; this includes people who have extended access outside of normal opening hours.

=== Light microscopes ===
{| class="wikitable"
|+
!Microscope
!Status
!Notes
!Date
|-
|[[Leica SP8X|SP8X]]
|OK
|
|
|-
|[[Leica SP8 Liachroic|SP8-Lia]]
|OK
|488 laser dodgy - don't turn it off!
|27.08.2025
|-
|[[Leica Thunder|Thunder]]
|OK
|
|
|-
|[[Leica Timelapse|Timelapse]]
|OK
|New camera installed
|25.09.2025
|-
|[[PhaseView light sheet|Lightsheet]]
|
|561 laser weak+ software out of date
Broken parts are sent for repair (PhaseView corp., Paris, France)
|03.10.2025
|-
|[[DM2500]]
|OK
|
|
|-
|[[Nikon sora|SoRa]]
|OK
|
|
|-
|[[Nikon TIRF widefield|TIRF]]
|OK
|
|
|-
|Spinoza server
|OK
|
|
|}

=== Electron microscopes and sample prep equipment ===
{| class="wikitable"
|+
!Machine
!Status
!Notes
!Date
|-
|[[JEOL1400 TEM|JEOL1400]]
|OK
|
|
|-
|[[JEOL2100 TEM|JEOL2100]]
|OK
|STEM detector broken - under repair
EDX detector broken
|aug 2024
pre 2023
|-
|[[Cryo-holder, cryo-dock and cryo-pumping station|Cryo-dock/station/holder]]
|OK
|
|
|-
|[[HPM100]]
|OK
|
|
|-
|[[EMPACT|EMpact]]
|Broken
|Unsure if can be fixed
|01.09.2025
|-
|[[Vitrobot]]
|OK
|
|
|-
|[[UC-E microtome]]
|Broken
|Under repair - contact Hetty if you need it soon
|01.09.2025
|-
|UC7/FC7 cryo-microtome
|OK
|
|
|-
|[[CCU-010]]
|OK
|
|
|-
|Edward306
|Broken
|Under repair
|
|-
|BAF400
|Broken
|Under repair
|
|-
|Vibratome
|OK
|
|
|-
|CPD-020
|In storage
|
|
|-
|JFD-030
|OK
|
|
|}

General Instrumentation Department

2025-11-03T09:53:33Z

Hetty: Kerst info erbij

The [https://www.ru.nl/en/departments/faculty-of-science/scientific-equipment-department General Instrumentation department] (GI department; Dutch: Gemeenschappelijk Instrumentarium) is a facility within the Faculty of Science at the Radboud University Nijmegen.

== Opening hours ==
The GI department is open on workdays from 8:00-18:00 (you do not need to badge in at the door). Contact us if you need access outside these hours.

==== Department closure during the Christmas holiday: from 22 Dec 2025 - 7 Jan 2026 ====
The Huygens building and therefor the GI department will be closed during the Christmas holiday from Monday 22 December onwards. Due to maintenance work on the Huygens building, this closure is extended up to including Wednesday January 7th. It is at the moment (03.11.2025) unclear if the microscopes need to be powered off during this time period. No one can the access the GI department during the Christmas closure period; this includes people who have extended access outside of normal opening hours.

== Radiation safety (TEMs) ==
The TEMs within the GI department are considered "Inherent Veilige Toestellen" (IVTs, 'inherently safe devices') by the radiation safety team. This means that they are safe to use. Please contact Hetty if you want to know more.

== Biosafety ==
Different labs within the GI department are operating at different biosafety levels. The biosafety level is noted next to each door.

===Biosafety levels in the GI department===
====SL-1====
* Most labs are SL-1.
* This means no work with GMO's or infectious agents takes place in these rooms.

====AP-1====
* We have two optional SL-1/AP-1 rooms:
** Room HG01.239 (containing the SP8x light microscope and the DM2500)
** Room HG01.236 (SP8-Lia)
* AP-1 essentially means that ML-1 samples can be imaged in this room, as long as the container (e.g. the microscope slide) with the sample remains closed at all times.
* Next to the lab door is a card which indicates whether or not GMO's are present in the room. Make sure to flip the card to the correct side when entering the room.

====ML-1====
* Room HG01.228 (TIRF, SoRa, Thunder) is an ML-1 room.
* Only authorised people are allowed to enter this room.

=== Rules regarding working in the ML-1 room (TIRF/SoRa/Thunder) ===
Please refer to the following documentation regarding how to work in the ML-1 room:

* [[:File:Werkvoorschriften deel3 GI Engels bvf.pdf|Work protocol GI, part 3 (English)]]
* [[:File:Werkvoorschriften deel3 GI NL bvf.pdf|Werkvoorschriften GI, deel 3 (Nederlands)]]
* [[:File:Checklist ruimteintro ML1 v1.pdf|Short summary of the key points]]

=== How to get access to the ML-1 room (TIRF/SoRa/Thunder) ===
Before you are allowed to enter the ML-1 lab, you have to complete a GI user registration. This consists of two parts:

* Fill in the GI's ML-1 user registration form. There are three versions of the form:
** [[:File:Intake form GI ML-I projectmedewerker 250728.pdf|A form for users that are registered as ‘projectmedewerkers’ in GRIMAS]]. They are allowed to work independently in the GI ML-1 room. (e.g. most PhD students)
** [[:File:Intake form GI ML-I student 250728.pdf|A form for ’students’]]. These users are not registered as ‘projectmedewerkers’ in GRIMAS, but are registered as ’students’ by their own department. They are allowed to “work under supervision” in the GI ML-1 room. (e.g. most MSc students)
** [[:File:Intake form GI ML-I guest 250728.pdf|A form for ‘guests’]]. These users need to be ‘one on one supervised’ in the GI ML-1 room at all times. (e.g. mechanics, microscope demonstrations/practicals).
* Attend a GI room-specific training by Jelle or Hetty. This takes about 5 minutes. If you receive a microscope training in this room, then the room-specific training is already included. After the training, Jelle or Hetty will sign off the form and archive it. You are now allowed to work in the ML-1 room.

=== Contact ===
For more information, comments or questions, contact Hetty ("Verantwoordelijk medewerker", VM), or Jelle ("Assistent verantwoordelijk medewerker", AVM).

Current microscope status

2025-10-16T13:41:02Z

Hetty: /* Electron microscopes and sample prep equipment */

=== Light microscopes ===
{| class="wikitable"
|+
!Microscope
!Status
!Notes
!Date
|-
|[[Leica SP8X|SP8X]]
|OK
|
|
|-
|[[Leica SP8 Liachroic|SP8-Lia]]
|OK
|488 laser dodgy - don't turn it off!
|27.08.2025
|-
|[[Leica Thunder|Thunder]]
|OK
|
|
|-
|[[Leica Timelapse|Timelapse]]
|OK
|New camera installed
|25.09.2025
|-
|[[PhaseView light sheet|Lightsheet]]
|
|561 laser weak+ software out of date
Broken parts are sent for repair (PhaseView corp., Paris, France)
|03.10.2025
|-
|[[DM2500]]
|OK
|
|
|-
|[[Nikon sora|SoRa]]
|OK
|
|
|-
|[[Nikon TIRF widefield|TIRF]]
|OK
|
|
|-
|Spinoza server
|OK
|
|
|}

=== Electron microscopes and sample prep equipment ===
{| class="wikitable"
|+
!Machine
!Status
!Notes
!Date
|-
|[[JEOL1400 TEM|JEOL1400]]
|OK
|
|
|-
|[[JEOL2100 TEM|JEOL2100]]
|OK
|STEM detector broken - under repair
EDX detector broken
|aug 2024
pre 2023
|-
|[[Cryo-holder, cryo-dock and cryo-pumping station|Cryo-dock/station/holder]]
|OK
|
|
|-
|[[HPM100]]
|OK
|
|
|-
|[[EMPACT|EMpact]]
|Broken
|Unsure if can be fixed
|01.09.2025
|-
|[[Vitrobot]]
|OK
|
|
|-
|[[UC-E microtome]]
|Broken
|Under repair - contact Hetty if you need it soon
|01.09.2025
|-
|UC7/FC7 cryo-microtome
|OK
|
|
|-
|[[CCU-010]]
|OK
|
|
|-
|Edward306
|Broken
|Under repair
|
|-
|BAF400
|Broken
|Under repair
|
|-
|Vibratome
|OK
|
|
|-
|CPD-020
|In storage
|
|
|-
|JFD-030
|OK
|
|
|}

Electron microscopy at the GI department

2025-10-16T13:39:27Z

Hetty: added equipment to list

This page lists the options for performing electron microscopy at the GI department.

=== List of equipment ===

==== Electron microscopes ====

* [[JEOL1400 TEM]]
* [[JEOL2100 TEM]]

==== Electron microscope sample holders and cryo-accessories ====

* Quick-change holder (2x)
* Quartet holder
* Single-tilt holder
* [[Cryo-holder, cryo-dock and cryo-pumping station]]
* Beryllium holder (for EDX)
* Dual axis room temperature tomography holder

==== Sample prep equipment ====

* Safematic [[CCU-010]] coater for glow discharging, carbon coating and sputter coating
* FEI [[Vitrobot]] plungefreezer
* Leica [[HPM100]] high-pressure freezer
* Leica [[EMPACT]] high-pressure freezer
* Reichert-Jung [[UC-E microtome]]
* Leica UC7/FC7 cryo-microtome
* Leica [[AFS1/AFS2]] freeze-substitution machines
* Leica Vibratome VT1000S
* EM KMR2 knife maker
* Balzers BAF400 freeze etcher
* Balzers CPD-020 critical point dryer
* Edwards 306 thermal evaporation coater

General Instrumentation Department

2025-09-29T12:06:51Z

Hetty:

The [https://www.ru.nl/en/departments/faculty-of-science/scientific-equipment-department General Instrumentation department] (GI department; Dutch: Gemeenschappelijk Instrumentarium) is a facility within the Faculty of Science at the Radboud University Nijmegen.

== Practical information ==
The GI department is open on workdays from 8:00-18:00. Contact us if you need access outside these hours.

== Radiation safety (TEMs) ==
The TEMs within the GI department are considered "Inherent Veilige Toestellen" (IVTs, 'inherently safe devices') by the radiation safety team. This means that they are safe to use. Please contact Hetty if you want to know more.

== Biosafety ==
Different labs within the GI department are operating at different biosafety levels. The biosafety level is noted next to each door.

===Biosafety levels in the GI department===
====SL-1====
* Most labs are SL-1.
* This means no work with GMO's or infectious agents takes place in these rooms.

====AP-1====
* We have two optional SL-1/AP-1 rooms:
** Room HG01.239 (containing the SP8x light microscope and the DM2500)
** Room HG01.236 (SP8-Lia)
* AP-1 essentially means that ML-1 samples can be imaged in this room, as long as the container (e.g. the microscope slide) with the sample remains closed at all times.
* Next to the lab door is a card which indicates whether or not GMO's are present in the room. Make sure to flip the card to the correct side when entering the room.

====ML-1====
* Room HG01.228 (TIRF, SoRa, Thunder) is an ML-1 room.
* Only authorised people are allowed to enter this room.

=== Rules regarding working in the ML-1 room (TIRF/SoRa/Thunder) ===
Please refer to the following documentation regarding how to work in the ML-1 room:

* [[:File:Werkvoorschriften deel3 GI Engels bvf.pdf|Work protocol GI, part 3 (English)]]
* [[:File:Werkvoorschriften deel3 GI NL bvf.pdf|Werkvoorschriften GI, deel 3 (Nederlands)]]
* [[:File:Checklist ruimteintro ML1 v1.pdf|Short summary of the key points]]

=== How to get access to the ML-1 room (TIRF/SoRa/Thunder) ===
Before you are allowed to enter the ML-1 lab, you have to complete a GI user registration. This consists of two parts:

* Fill in the GI's ML-1 user registration form. There are three versions of the form:
** [[:File:Intake form GI ML-I projectmedewerker 250728.pdf|A form for users that are registered as ‘projectmedewerkers’ in GRIMAS]]. They are allowed to work independently in the GI ML-1 room. (e.g. most PhD students)
** [[:File:Intake form GI ML-I student 250728.pdf|A form for ’students’]]. These users are not registered as ‘projectmedewerkers’ in GRIMAS, but are registered as ’students’ by their own department. They are allowed to “work under supervision” in the GI ML-1 room. (e.g. most MSc students)
** [[:File:Intake form GI ML-I guest 250728.pdf|A form for ‘guests’]]. These users need to be ‘one on one supervised’ in the GI ML-1 room at all times. (e.g. mechanics, microscope demonstrations/practicals).
* Attend a GI room-specific training by Jelle or Hetty. This takes about 5 minutes. If you receive a microscope training in this room, then the room-specific training is already included. After the training, Jelle or Hetty will sign off the form and archive it. You are now allowed to work in the ML-1 room.

=== Contact ===
For more information, comments or questions, contact Hetty ("Verantwoordelijk medewerker", VM), or Jelle ("Assistent verantwoordelijk medewerker", AVM).

Light microscopy

2025-09-29T12:03:52Z

Hetty: Added link

This page lists the options for performing light microscopy at the GI department.

=== List of equipment ===

==== Light microscopes ====

* [[Leica SP8X|Leica SP8X live-cell confocal]]
* [[Leica SP8 Liachroic|Leica SP8 liachroic confocal]]
* [[Leica Thunder|Leica "Thunder" widefield]]
* [[Leica Timelapse|Leica "Timelapse" widefield]]
* [[PhaseView light sheet|PhaseView Alpha3 light sheet]]
* [[DM2500|Leica DM2500 upright widefield]]

* [[Nikon TIRF widefield]]
* [[Nikon sora|Nikon SoRa spinning disc]]

==== Software packages and other tools ====

* Spinoza image analysis server
* Huygens
* Microfluidics pump for inverted microscopes

=== External links ===
[https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-light-microscopy-image-analysis All microscopes (booking system)]

DM2500

2025-09-29T12:03:18Z

Hetty: Started page

The Leica-Microsystems DM2500 microscope present in room HG01.228 is an upright microscope equipped for imaging in transmission (bright field, phase-contrast [10-100x], dark-field [from 10-40x]) and fluorescence mode.

== Manuals and user guides ==

== Current status ==
The current status of the microscope can be found [[Current microscope status#Light microscopes|here]] and on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-light-microscopy-image-analysis booking website].

== Biosafety and access ==
The SP8-Lia is located in an AP-1 room. See the [[General Instrumentation Department#Biosafety|Biosafety]] section on rules regarding working in this room.

== Technical specifications ==
The Leica-Microsystems DM2500 microscope present in room HG01.228 is an upright microscope equipped for imaging in transmission (bright field, phase-contrast [10-100x], dark-field [from 10-40x]) and fluorescence mode.

Objectives with magnification 2.5, 10, 20, 40 and 100x are available. Images can be recorded with a DCF7000T Leica sensitive color camera (up to 1920x1440 pixels) that can be operated for bright-field, but also fluorescence, phase-contrast and dark-field wide-field microscopy. Freely definable ROIs in combination with binning are possible.

Other functions beside simple acquisition of images involve image averaging, shading corrections,sharpening with active noise reduction, white and black balance, HDR acquisition, time lapse imaging and streaming mode.

The camera works together with the LASX software. The modules for image overlays, time-lapse and video streaming are present.

Fluorescent filters mounted on the system are:

* A (excitation: 340-380 nm, emission: >425)
* I3 (450-490, >515)
* N2.1 (515-560, >590)
* Y5 (590-650, 662-738)

Current microscope status

2025-09-29T12:01:34Z

Hetty: Added link

=== Light microscopes ===
{| class="wikitable"
|+
!Microscope
!Status
!Notes
!Date
|-
|[[Leica SP8X|SP8X]]
|OK
|
|
|-
|[[Leica SP8 Liachroic|SP8-Lia]]
|OK
|488 laser dodgy - don't turn it off!
|27.08.2025
|-
|[[Leica Thunder|Thunder]]
|OK
|
|
|-
|[[Leica Timelapse|Timelapse]]
|OK
|New camera installed
|25.09.2025
|-
|[[PhaseView light sheet|Lightsheet]]
|
|561 laser weak
Software out of date

service visit planned 03.10.2025
|?
|-
|[[DM2500]]
|OK
|
|
|-
|[[Nikon sora|SoRa]]
|OK
|
|
|-
|[[Nikon TIRF widefield|TIRF]]
|OK
|
|
|-
|Spinoza server
|OK
|
|
|}

=== Electron microscopes and sample prep equipment ===
{| class="wikitable"
|+
!Machine
!Status
!Notes
!Date
|-
|[[JEOL1400 TEM|JEOL1400]]
|OK
|
|
|-
|[[JEOL2100 TEM|JEOL2100]]
|OK
|STEM detector broken - under repair
EDX detector broken
|aug 2024
pre 2023
|-
|[[Cryo-holder, cryo-dock and cryo-pumping station|Cryo-dock/station/holder]]
|OK
|
|
|-
|[[HPM100]]
|OK
|
|
|-
|[[EMPACT|EMpact]]
|Broken
|Unsure if can be fixed
|01.09.2025
|-
|[[Vitrobot]]
|OK
|
|
|-
|[[UC-E microtome]]
|Broken
|Under repair - contact Hetty if you need it soon
|01.09.2025
|-
|UC7/FC7 cryo-microtome
|OK
|
|
|-
|[[CCU-010]]
|OK
|
|
|-
|Edward306
|Broken
|Under repair
|
|-
|BAF400
|Broken
|Under repair
|
|-
|Vibratome
|OK
|
|
|-
|
|
|
|
|}

Current microscope status

2025-09-29T12:00:07Z

Hetty: Added link

=== Light microscopes ===
{| class="wikitable"
|+
!Microscope
!Status
!Notes
!Date
|-
|[[Leica SP8X|SP8X]]
|OK
|
|
|-
|[[Leica SP8 Liachroic|SP8-Lia]]
|OK
|488 laser dodgy - don't turn it off!
|27.08.2025
|-
|[[Leica Thunder|Thunder]]
|OK
|
|
|-
|[[Leica Timelapse|Timelapse]]
|OK
|New camera installed
|25.09.2025
|-
|[[PhaseView light sheet|Lightsheet]]
|
|561 laser weak
Software out of date

service visit planned 03.10.2025
|?
|-
|DM2500
|OK
|
|
|-
|[[Nikon sora|SoRa]]
|OK
|
|
|-
|[[Nikon TIRF widefield|TIRF]]
|OK
|
|
|-
|Spinoza server
|OK
|
|
|}

=== Electron microscopes and sample prep equipment ===
{| class="wikitable"
|+
!Machine
!Status
!Notes
!Date
|-
|[[JEOL1400 TEM|JEOL1400]]
|OK
|
|
|-
|[[JEOL2100 TEM|JEOL2100]]
|OK
|STEM detector broken - under repair
EDX detector broken
|aug 2024
pre 2023
|-
|[[Cryo-holder, cryo-dock and cryo-pumping station|Cryo-dock/station/holder]]
|OK
|
|
|-
|[[HPM100]]
|OK
|
|
|-
|[[EMPACT|EMpact]]
|Broken
|Unsure if can be fixed
|01.09.2025
|-
|[[Vitrobot]]
|OK
|
|
|-
|[[UC-E microtome]]
|Broken
|Under repair - contact Hetty if you need it soon
|01.09.2025
|-
|UC7/FC7 cryo-microtome
|OK
|
|
|-
|[[CCU-010]]
|OK
|
|
|-
|Edward306
|Broken
|Under repair
|
|-
|BAF400
|Broken
|Under repair
|
|-
|Vibratome
|OK
|
|
|-
|
|
|
|
|}

PhaseView light sheet

2025-09-29T11:59:30Z

Hetty: Started page

PhaseView/Evident light sheet microscope with customized sample holders (in SL-1 room).

== Manuals and user guides ==

== Current status ==
The current status of the microscope can be found [[Current microscope status#Light microscopes|here]] and on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-light-microscopy-image-analysis booking website].

== Biosafety and access ==
The Timelapse microscope is located in an SL-1 room. GMO's are not allowed in this room.

== Technical specifications ==

=== Microscope ===

* Manual upright Olympus BX43F microscope

=== Excitation ===
Dual light sheet illumination through two 10x/0.25NA long distance Olympus objectives using a 4-laser combiner of the following laser lines:

* 405nm/50mW
* 488nm/50mW
* 561nm/50mW
* 638nm/100mW

=== Emission Selection ===
The system has the following filters mounted on a motorized filter wheel:

* ET440/40 nm
* ET525/50
* ET600/50
* ET690/50
* Notch filter 405/488/561/638

=== Detection ===
ORCA-FLASH4.0V3

* Scientific CMOS Sensor 2048 (H)×2048 (V), 6.5 μm×6.5 μm
* QE 82 % (@560 nm)
* Format 13.312 mm×13.312 mm
* Camera Link interface (100fps)

=== Objectives ===

* 10x/0.3 Water dipping long distance
* 20x/0.5 Water dipping long distance
* 40x/0.8 Water dipping long distance

=== Chamber and Sample holders ===
Chamber dimensions: width 21mm, length 70m height 25mm. Sample size up to 10 x 10 x 10 mm, cuvette filled with watery refractive index media (volume < 15ml. Agarose strips containing sampes can be mounted in water and observed straight away.

=== Motorized Rotation Module ===
Motorized rotation module with 1024 steps resolution, software controlled.

=== XY Tiling ===
XY motorized stage with 15mm range and 0.1um precision. Software controlled

=== Software ===
QtSPIM software for image acquisition XY, Z, channels, t (time), θ (rotation) and tiling

Light microscopy

2025-09-29T11:56:31Z

Hetty: Added link

This page lists the options for performing light microscopy at the GI department.

=== List of equipment ===

==== Light microscopes ====

* [[Leica SP8X|Leica SP8X live-cell confocal]]
* [[Leica SP8 Liachroic|Leica SP8 liachroic confocal]]
* [[Leica Thunder|Leica "Thunder" widefield]]
* [[Leica Timelapse|Leica "Timelapse" widefield]]
* [[PhaseView light sheet|PhaseView Alpha3 light sheet]]
* Leica DM2500 upright widefield

* [[Nikon TIRF widefield]]
* [[Nikon sora|Nikon SoRa spinning disc]]

==== Software packages and other tools ====

* Spinoza image analysis server
* Huygens
* Microfluidics pump for inverted microscopes

=== External links ===
[https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-light-microscopy-image-analysis All microscopes (booking system)]

Leica Timelapse

2025-09-29T11:53:13Z

Hetty: /* Technical specifications */

Leica DMi8 inverted widefield epifluorescence microscope with phase contrast, colour camera, monochrome camera (in SL-1 room)

== Manuals and user guides ==

== Current status ==
The current status of the microscope can be found [[Current microscope status#Light microscopes|here]] and on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-light-microscopy-image-analysis booking website].

== Biosafety and access ==
The Timelapse microscope is located in an SL-1 room. GMO's are not allowed in this room.

== Technical specifications ==
===Camera's===
* DMC4500 colour camera
* DFC9000GT monochrome camera

===Objectives===
* 2.5x/0.07 dry
* 10x/0.30 dry
* 20x/0.70 dry UV
* 63x/1.40 oil
* 100x/1.40 oil

===Filters===
* DAPI: excitation: 327-383 nm, emission: 435-485 nm
* GFP: 450-490, 500-550
* CFP: 426-446, 460-500
* Y3: 532-558, 570-640
* Y5: 590-650, 662-738
Available: FITC_LP: 450-490, >515

===Other===
* Temperature incubation
* 1.0 - 1.6 - 2.0 x magnification lens

Leica Timelapse

2025-09-29T11:52:29Z

Hetty:

Leica DMi8 inverted widefield epifluorescence microscope with phase contrast, colour camera, monochrome camera (in SL-1 room)

== Manuals and user guides ==

== Current status ==
The current status of the microscope can be found [[Current microscope status#Light microscopes|here]] and on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-light-microscopy-image-analysis booking website].

== Biosafety and access ==
The Timelapse microscope is located in an SL-1 room. GMO's are not allowed in this room.

== Technical specifications ==
===Camera's===
* DMC4500 colour camera
* DFC9000GT monochrome camera

===Objectives===
* 2.5x/0.07 dry
* 10x/0.30 dry
* 20x/0.70 dry UV
* 63x/1.40 oil
* 100x/1.40 oil

===Filters===
* DAPI: excitation: 327-383 nm, emission: 435-485 nm
* GFP: 450-490, 500-550
* CFP: 426-446, 460-500
* Y3: 532-558, 570-640
* Y5: 590-650, 662-738

===Other===
* Available: FITC_LP: 450-490, >515
* Temperature incubation
* 1.0 - 1.6 - 2.0 x magnification lens

Leica Timelapse

2025-09-29T11:52:06Z

Hetty:

Leica DMi8 inverted widefield epifluorescence microscope with phase contrast, colour camera, monochrome camera (in SL-1 room)

== Manuals and user guides ==

== Current status ==
The current status of the microscope can be found [[Current microscope status#Light microscopes|here]] and on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-light-microscopy-image-analysis booking website].

== Biosafety and access ==
The SoRa is located in an SL-1 room. GMO's are not allowed in this room.

== Technical specifications ==
===Camera's===
* DMC4500 colour camera
* DFC9000GT monochrome camera

===Objectives===
* 2.5x/0.07 dry
* 10x/0.30 dry
* 20x/0.70 dry UV
* 63x/1.40 oil
* 100x/1.40 oil

===Filters===
* DAPI: excitation: 327-383 nm, emission: 435-485 nm
* GFP: 450-490, 500-550
* CFP: 426-446, 460-500
* Y3: 532-558, 570-640
* Y5: 590-650, 662-738

===Other===
* Available: FITC_LP: 450-490, >515
* Temperature incubation
* 1.0 - 1.6 - 2.0 x magnification lens

Current microscope status

2025-09-29T11:51:02Z

Hetty: Added link

=== Light microscopes ===
{| class="wikitable"
|+
!Microscope
!Status
!Notes
!Date
|-
|[[Leica SP8X|SP8X]]
|OK
|
|
|-
|[[Leica SP8 Liachroic|SP8-Lia]]
|OK
|488 laser dodgy - don't turn it off!
|27.08.2025
|-
|[[Leica Thunder|Thunder]]
|OK
|
|
|-
|[[Leica Timelapse|Timelapse]]
|OK
|New camera installed
|25.09.2025
|-
|Lightsheet
|
|561 laser weak
Software out of date

service visit planned 03.10.2025
|?
|-
|DM2500
|OK
|
|
|-
|[[Nikon sora|SoRa]]
|OK
|
|
|-
|[[Nikon TIRF widefield|TIRF]]
|OK
|
|
|-
|Spinoza server
|OK
|
|
|}

=== Electron microscopes and sample prep equipment ===
{| class="wikitable"
|+
!Machine
!Status
!Notes
!Date
|-
|[[JEOL1400 TEM|JEOL1400]]
|OK
|
|
|-
|[[JEOL2100 TEM|JEOL2100]]
|OK
|STEM detector broken - under repair
EDX detector broken
|aug 2024
pre 2023
|-
|[[Cryo-holder, cryo-dock and cryo-pumping station|Cryo-dock/station/holder]]
|OK
|
|
|-
|[[HPM100]]
|OK
|
|
|-
|[[EMPACT|EMpact]]
|Broken
|Unsure if can be fixed
|01.09.2025
|-
|[[Vitrobot]]
|OK
|
|
|-
|[[UC-E microtome]]
|Broken
|Under repair - contact Hetty if you need it soon
|01.09.2025
|-
|UC7/FC7 cryo-microtome
|OK
|
|
|-
|[[CCU-010]]
|OK
|
|
|-
|Edward306
|Broken
|Under repair
|
|-
|BAF400
|Broken
|Under repair
|
|-
|Vibratome
|OK
|
|
|-
|
|
|
|
|}

Leica Timelapse

2025-09-29T11:50:20Z

Hetty:

Leica DMi8 inverted widefield epifluorescence microscope with phase contrast, colour camera, monochrome camera (in SL-1 room)

== Manuals and user guides ==

== Current status ==
The current status of the microscope can be found [[Current microscope status#Light microscopes|here]] and on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-light-microscopy-image-analysis booking website].

== Technical specifications ==

===Camera's===
* DMC4500 colour camera
* DFC9000GT monochrome camera

===Objectives===
* 2.5x/0.07 dry
* 10x/0.30 dry
* 20x/0.70 dry UV
* 63x/1.40 oil
* 100x/1.40 oil

===Filters===
* DAPI: excitation: 327-383 nm, emission: 435-485 nm
* GFP: 450-490, 500-550
* CFP: 426-446, 460-500
* Y3: 532-558, 570-640
* Y5: 590-650, 662-738

===Other===
* Available: FITC_LP: 450-490, >515
* Temperature incubation
* 1.0 - 1.6 - 2.0 x magnification lens

Leica Timelapse

2025-09-29T11:48:19Z

Hetty: Created page with " Leica DMi8 inverted widefield epifluorescence microscope with phase contrast, colour camera, monochrome camera (in SL-1 room) == Manuals and user guides == == Current status == The current status of the microscope can be found here and on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-light-microscopy-image-analysis booking website]. == Technical specifications =="

Light microscopy

2025-09-29T11:46:26Z

Hetty: Added link

This page lists the options for performing light microscopy at the GI department.

=== List of equipment ===

==== Light microscopes ====

* [[Leica SP8X|Leica SP8X live-cell confocal]]
* [[Leica SP8 Liachroic|Leica SP8 liachroic confocal]]
* [[Leica Thunder|Leica "Thunder" widefield]]
* [[Leica Timelapse|Leica "Timelapse" widefield]]
* PhaseView Alpha3 light sheet
* Leica DM2500 upright widefield

* [[Nikon TIRF widefield]]
* [[Nikon sora|Nikon SoRa spinning disc]]

==== Software packages and other tools ====

* Spinoza image analysis server
* Huygens
* Microfluidics pump for inverted microscopes

=== External links ===
[https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-light-microscopy-image-analysis All microscopes (booking system)]