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Tutorial:

How to use the UC2 infinity-corrected microscope?

Version: 2020-08-11

This tutorial correpsonds to the Nvidia Jetson GUI in our Software-Branch.

Connect to the Jetson

The current Jetson Nano runs with Linux (Ubuntu). You can connect to it using SSH. The easiest is to create a WiFi Hotspot with an Android (tested, possibly also iPHONE) cellphone. Connect your computer (e.g. MAC/Windows) as well as the Jetson to it.

MAC

  • Open the terminal
cd /home/bene/Downloads/UC2-Software-GIT/GUI/RASPBERRY_PI/RASPIapp_py3
export DISPLAY=:0
python main.py

Windows

  • Download and install WinSCP + Putty
  • open Putty and connect to the Nvidia Jetson Nano; Use its IP which can be determined by typing ifconfig into the terminal

expected output:

[INFO   ] [Logger      ] Record log in /home/bene/.kivy/logs/kivy_20-08-11_5.txt
[INFO   ] [Kivy        ] v2.0.0rc3, git-9ff5f12, 20200803
[INFO   ] [Kivy        ] Installed at "/home/bene/.local/lib/python3.7/site-packages/kivy/__init__.py"
[INFO   ] [Python      ] v3.7.5 (default, Nov  7 2019, 10:50:52) 
[GCC 8.3.0]
[INFO   ] [Python      ] Interpreter at "/usr/bin/python3.7"
[INFO   ] [Factory     ] 186 symbols loaded
[INFO   ] [Image       ] Providers: img_tex, img_dds, img_sdl2, img_pil (img_ffpyplayer ignored)
[INFO   ] [Text        ] Provider: sdl2(['text_pango'] ignored)
[INFO   ] [Window      ] Provider: sdl2
dbus[8533]: arguments to dbus_message_new_method_call() were incorrect, assertion "path != NULL" failed in file ../../../dbus/dbus-message.c line 1362.
This is normally a bug in some application using the D-Bus library.

[INFO   ] [GL          ] Using the "OpenGL" graphics system
[INFO   ] [GL          ] Backend used <gl>
[INFO   ] [GL          ] OpenGL version <b'4.6.0 NVIDIA 32.3.1'>
[INFO   ] [GL          ] OpenGL vendor <b'NVIDIA Corporation'>
[INFO   ] [GL          ] OpenGL renderer <b'NVIDIA Tegra X1 (nvgpu)/integrated'>
[INFO   ] [GL          ] OpenGL parsed version: 4, 6
[INFO   ] [GL          ] Shading version <b'4.60 NVIDIA'>
[INFO   ] [GL          ] Texture max size <16384>
[INFO   ] [GL          ] Texture max units <32>
[INFO   ] [Window      ] auto add sdl2 input provider
[INFO   ] [Window      ] virtual keyboard not allowed, single mode, not docked
ERROR: Could not import scipy!
[ DEBUG    ] [ UC2           ] Logging successfully initialized to -> uc2-20200811_122326.log
Configuration file loaded

alternative double-click on the icon on the Desktop startUC2.sh.

Getting started

UC2 GUI

The GUI has the following functionalities:

- BURST: Take fluorescent images at "high-speed" (T=0.5s)
- Preview: Observe the image using the preview window 
- Long-Term experiments: Take fluorescent and/or brightfield images sequentially (T>1s, multiple days)
- Hardware control: X/Y/Z, Laser intensity, LED on/off

Quick tour:

BURST-Mode (T<1s)

You can take fluorescent images at a rate of 0.5 s by first (!) pressing the button "BURST", then hit "Start Preview". The images will be saved in the Folder DATA with a unique name which follows the current date.

Long-term Acquisitions (T>1s)

For long-term image series where you want to have multi-modal imaging capabilities (e.g. BF+FLUO), you can hit "Start Experiment" and choose the period and length of the experiment. Then select Fluo and/or BF and start the experiment. The images are saved in the folder data.

Hardware Control

XYZ-Stage

The deltastage from the openflexure project can be controlled by first typing the direction button (e.g. X) and then drive back/forth. You can vary the step-size by pressing --/++. The stage may wobble, we will update that soon!

Fluorscence (Laser)

The button FLUO activates the laser which can be controled in intensity. Therefore move the slider until you get the right intensity in the sample plane.

Brightfield

The button FULL activates the LED.

Vimba Viewer

You can start the VIMBA-Viewer by double clicking the Icon startVimbaViewer.shon the Desktop. It starts the GUI to have full control over the camera:

Align the setup

  1. Mount the LED with this tripod mechanism so that it's in the center of the Objective lens
  2. Follow the path of the transmitted light until . It has to go tr

Mount the sample

Focus the sample

Downloading Data

BURST Data

The data can be found in the folder ./DATA

Long-term Data

The data can be found in the folder ./data

Trouble Shooting

If nothing is woking

  • Did you turn it off and on again?

Autofocus does not work

  • This feature is currently not implemented in the Alvium Camera framework