Merge branch 'master' of https://github.com/bionanoimaging/UC2-GIT

APPLICATIONS/APP_Fluorescence_Microscope_infinity/Readme.md

@@ -92,6 +92,17 @@ This setup has only a z-stage
 To make it more stable you can "sandwich" it with a second baseplate | <img src="./IMAGES/Application_Fluorescence_Micrsocope_Infinity_openflexure_sandwich.png" width=500>  
 
 
+
+**Assembled Setups with a Jetson-driven mono camera:**
+
+For more infos about the camera look [here](../../CAD/ASSEMBLY_CUBE_AlliedVision_Alvium) 
+
+<img src="./IMAGES/photo_setup_1.jpg" width=500> 
+
+<img src="./IMAGES/photo_setup_2.jpg" width=500> 
+
+
+## Parts
 in List form:
 
 | Amount | Type                                      | Properties                        | Price  | Source                                                                                                                                                                    |
@@ -135,6 +146,24 @@ This is a set of ATTO 647 labelled *e.colis* provided by O. Helle from UiO image
 <img src="./IMAGES/1.25NA_100x_ecoli_p20pro.jpg" width="500">
 </p>
 
+This is acquired with the Allied Vision Alvium 1500-158 and the new UC2 Nvidia Jetson Nano GUI. HeLa labelled with Alexa Fluor 647 Phal.
+
+***Brightfield***
+<p align="center">
+<img src="./IMAGES/20200810-MEAS-Bright--1.jpg-1.jpg" width="500">
+</p>
+
+***Fluorescence***
+<p align="center">
+<img src="./IMAGES/20200810-MEAS-Fluor--INT_20-1.jpg" width="500">
+</p>
+
+***Overlay***
+<p align="center">
+<img src="./IMAGES/HeLa_AF647_BF_Overlay.png" width="500">
+</p>
+
+
 ## <img src="./IMAGES/S.png" width="40"> Participate!
 
 Do you want to show your own results? Do you have ideas for improvements? Let us know!

APPLICATIONS/APP_Fluorescence_Microscope_infinity/Tutorial.md

@@ -0,0 +1,146 @@
+# 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](https://github.com/bionanoimaging/UC2-Software-GIT). 
+
+### 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:*
+
+<p align="center">
+<img src="./IMAGES/Tutorial_GUI.gif" width="400" alt="">
+</p> 
+
+#### 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.sh```on the Desktop. It starts the GUI to have full control over the camera:
+
+<p align="center">
+<img src="./IMAGES/vimba_3.png" width="400" alt="">
+</p> 
+
+
+## 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
+
+
+
+