Many updates, also a number of empty pages deleted

Author: Gabriella Turek

2013-06-18_-_SPIMage_processing_tutorials.md

@@ -1,35 +1,16 @@
 ---
 ---
-Integral part of SPIM imaging is data processing sometimes referred to
-as **SPIMage processing**. The OpenSPIM project relies on tight
-integration with [Fiji](http://fiji.sc) where most of the algorithms for
-SPIMage processing have been implemented in the past.
+Integral part of SPIM imaging is data processing sometimes referred to as **SPIMage processing**. The OpenSPIM project relies on tight integration with [Fiji](https://fiji.sc) where most of the algorithms for SPIMage processing have been implemented in the past.
 
-We have assembled [**extensive
-tutorials**](Operation#Data_processing "wikilink") that will walk you
-through all the steps required to put multi-view SPIM data together.
+We have assembled [**extensive tutorials**](Operation#Data_processing) that will walk you through all the steps required to put multi-view SPIM data together.
 
-  - We start by defining [**System
-    requirements**](Pre-requisites "wikilink") and downloading
-    ['''sample OpenSPIM data](Raw_data "wikilink"),
-  - followed by optional [**pre-processing
-    steps**](Pre-processing "wikilink").
-  - [**Multi-view registration**](Registration "wikilink") is at the
-    heart of SPIMage processing pipeline.
-  - [**Multi-view Fusion**](Fusion "wikilink") section discusses how to
-    combine several view into one output image
-  - [**Time series registration**](Timelapse_Registration "wikilink")
-    removes the sample drift across long-term timelapse.
+  - We start by defining [**System requirements**](Pre-requisites) and downloading [sample OpenSPIM data](Raw_data), - followed by optional [**pre-processing steps**](Pre-processing).
+  - [**Multi-view registration**](Registration) is at the heart of SPIMage processing pipeline.
+  - [**Multi-view Fusion**](Fusion) section discusses how to combine several view into one output image
+  - [**Time series registration**](Timelapse_Registration) removes the sample drift across long-term timelapse.
 
-The pipeline is relatively linear as described above, we highlight the
-steps where [**alternative routes
-exist**](Registration#Cross-road_in_SPIM_plugins "wikilink").
+The pipeline is relatively linear as described above, we highlight the steps where [**alternative routes exist**](Registration#cross-road_in_spim_plugins).
 
-Theoretical principles of the methods involved are best described on the
-[SPIM pages of Fiji wiki](http://fiji.sc/SPIM_Registration).
+Theoretical principles of the methods involved are best described on the [SPIM pages of Fiji wiki](https://fiji.sc/SPIM_Registration).
 
-The description of several steps of the SPIMage processing pipeline are
-still in the works. Particularly [**multi-view
-deconvolution**](Fusion#Deconvolution "wikilink"), [**data
-viewing**](Browsing "wikilink") and [**3D
-rendering**](3D_rendering "wikilink"). Stay tuned.
+The description of several steps of the SPIMage processing pipeline are still in the works. Particularly [**multi-view deconvolution**](Fusion#deconvolution), [**data viewing**](https://fiji.sc/BigDataViewer) and [**3D rendering**](3D_rendering). Stay tuned.

Arduino_based_camera-laser_synchronization_system.md

@@ -2,119 +2,77 @@
 ---
 ## Principle of operation
 
-We assume that the camera is controlled by the computer via the API or
-other means and that it is configured such that one of its IO pins
-reports the integration interval. We will call this signal CINT. This
-pin is at 0V when not integrating and +5V when integrating. Depending on
-the camera model this can be reversed.
-
-We assume that the laser has a digital IO port for binary control of
-intensity. We will call this signal LT. The laser illumination is then
-synchronized to the camera integration interval by generating the
-appropriate LT signal according to the incoming CINT signal. Two
-variables can be adjusted: delay and duration. Delay is how many
-microseconds separate the start of aquisition and the switching of the
-laser to on state. And duration is, well, how long in microseconds the
-laser remains on.
-
-This parameters are sent as serial commands to the Arduino. For example,
-sending the following string: 'l=0,d=1000' sets the delay to zero ms and
-duation to 1000 mus = 1 ms.
+We assume that the camera is controlled by the computer via the API or other means and that it is configured such that one of its IO pins reports the integration interval. We will call this signal CINT. This pin is at 0V when not integrating and +5V when integrating. Depending on the camera model this can be reversed.
+
+We assume that the laser has a digital IO port for binary control of intensity. We will call this signal LT. The laser illumination is then synchronized to the camera integration interval by generating the appropriate LT signal according to the incoming CINT signal. Two variables can be adjusted: delay and duration. Delay is how many microseconds separate the start of acquisition and the switching of the laser to on state. And duration is, well, how long in microseconds the laser remains on.
+
+This parameters are sent as serial commands to the Arduino. For example, sending the following string: 'l=0,d=1000' sets the delay to zero ms and duration to 1000 mus = 1 ms.
 
 ## Arduino Wiring
 
-<span style="color:#FF0000">Rule zero of electronics: check your wirings
-several times, and in different ways, before powering up, there is no
-undo\! When it's burned it's burned\!</span>
+<span style="color:#FF0000">Rule zero of electronics: check your wirings several times, and in different ways, before powering up, there is no undo! When it's burned it's burned!</span>
 
 In the following, inputs and outputs are relative to the Arduino:
 
   - Camera pins:
-      - pinCSB --\> Camera SYNC-B/Strobe pin (input)
-
-<!-- end list -->
+      - pinCSB -> Camera SYNC-B/Strobe pin (input)
 
   - Laser pins:
-      - pinLT 4 --\> Laser Trigger (output)
+      - pinLT 4 -> Laser Trigger (output)
 
 Below is an overview diagram of the very simple wiring needed:
-![OverviewCircuit.png](OverviewCircuit.png "OverviewCircuit.png")
-
-It is often the case that the internal camera/laser electronics are
-protected against electronic noise or damage by
-[optocouplers](http://en.wikipedia.org/wiki/Optocouplers). Optocouplers
-are essentially an optical form of [galvanic
-isolation](http://en.wikipedia.org/wiki/Galvanic_isolation): it's a
-optical bridge that lets the signal go through without any current flow.
-Such a device needs electric current to function, and by definition this
-current cannot come from the camera/laser itself otherwise that would
-defeat the purpose of the optocoupler... To cut a long story short, you
-need to check whether the IO interface of the camera/laser needs to be
-supplied with DC current (most likely +5V). In any case you will also
-need to connect the GND (ground) to your 0V on the Arduino. For that you
-can use the +5V and 0V GND pins of the Arduino. It is a general rule
-that all grounds of communicating devices to be shorted together.
-
-<span style="color:#FF0000">Rule one of digital electronics: when in
-doubt about the amount of current sinked or sourced by a pin and about
-tolerances, it is a good idea to 1) read the manual again and check how
-much an output pin can source, and what is the impedance of an input
-pin, 2) to add a resistor (200 Ohm) in series to limit current flow,
-just in case... </span>
+
+{% include image src="OverviewCircuit.png" width="70%" caption="" %}
+
+It is often the case that the internal camera/laser electronics are protected against electronic noise or damage by [optocouplers](https://en.wikipedia.org/wiki/Optocouplers). Optocouplers are essentially an optical form of [galvanic
+isolation](https://en.wikipedia.org/wiki/Galvanic_isolation): it's an optical bridge that lets the signal go through without any current flow. Such a device needs electric current to function, and by definition this current cannot come from the camera/laser itself otherwise that would defeat the purpose of the optocoupler... To cut a long story short, you need to check whether the IO interface of the camera/laser needs to be supplied with DC current (most likely +5V). In any case you will also need to connect the GND (ground) to your 0V on the Arduino. For that you can use the +5V and 0V GND pins of the Arduino. It is a general rule that all grounds of communicating devices to be shorted together.
+
+<span style="color:#FF0000">Rule one of digital electronics: when in doubt about the amount of current sinked or sourced by a pin and about tolerances, it is a good idea to 1) read the manual again and check how much an output pin can source, and what is the impedance of an input pin, 2) to add a resistor (200 Ohm) in series to limit current flow, just in case... </span>
 
 ## Camera Wiring
 
-Here we detail how to use the synchronization system for the SonyXCD
-cameras. As explained above, and as shown in the diagram below, most
-cameras IO interfaces have an optocoupler - thus you have to connect GND
-pins to ground and DC IN pins to +5V.
+Here we detail how to use the synchronization system for the SonyXCD cameras. As explained above, and as shown in the diagram below, most cameras IO interfaces have an optocoupler - thus you have to connect GND pins to ground and DC IN pins to +5V.
 
-This distracting detail aside, the really interesting pin is STROBE OUT
-which is our CINT pin and which tells us when the camera is acquiring.
-SonyXCD cameras output 0V when acquiring and +5V when not. This is
-different from Retiga-SRV cameras for example that output the opposite
-signal.
+This distracting detail aside, the really interesting pin is STROBE OUT which is our CINT pin and which tells us when the camera is acquiring. SonyXCD cameras output 0V when acquiring and +5V when not. This is different from Retiga-SRV cameras for example that output the opposite signal.
 
-![SonyXCD12pin.png](SonyXCD12pin.png "SonyXCD12pin.png")
+{% include image src="SonyXCD12pin.png" width="70%" caption="" %}
 
 ## Laser Wiring
 
-Wiring the laser is usually much easier, you just need a diftal IO pin
-that gives access to a binary control of the laser. For example, for the
-Coherent CUBE lasers this is called "digital enable".
+Wiring the laser is usually much easier, you just need a diftal IO pin that gives access to a binary control of the laser. For example, for the Coherent CUBE lasers this is called "digital enable".
 
 ## Arduino Sketch
 
 Below is the current version of the Arduino sketch:
 
-``` cpp
- // OpenSPIM laser/camera synchronization based on Arduino
+<pre>
+// OpenSPIM laser/camera synchronization based on Arduino
 // Loic Royer
 
 // The principle of operation is simple:
-// We assume that the camera is controlled by the computer via the API 
-// or other means and that the CINT signal reports the integration time 
-// interval. In other words the CINT pin on the camera tells us when the 
+// We assume that the camera is controlled by the computer via the API
+// or other means and that the CINT signal reports the integration time
+// interval. In other words the CINT pin on the camera tells us when the
 // camera is aquiring (excluding the read-out time).
 // On the laser side, we assume that the laser is in pulse mode.
 //
-// The laser is then controlled in a "slave" mode. This program synchronizes 
+// The laser is then controlled in a "slave" mode. This program synchronizes
 // the laser to the camera aquisition.
 // Two variables can be adjusted via a simple serial protocol: delay and duration.
 // Delay is how many microseconds between start of aquisition and laser on have elapsed,
-// and duration is, well, how long the laser is on in microseconds. 
-// sending the following string: 'l=0,d=1000' sets the delay to zero ms 
+// and duration is, well, how long the laser is on in microseconds.
+// sending the following string: 'l=0,d=1000' sets the delay to zero ms
 // and duation to 1000 mus = 1 ms
 
 // in the following, inputs and outputs are relative to the arduino
 // Camera pins:
 #define pinCINT 2// Camera integration signal pin (input)
 
-// Laser pins: 
-//Important: In the case of the Coherent laser CUBE system, 
+// Laser pins:
+//Important: In the case of the Coherent laser CUBE system,
 // the control box BNC connector has an input impedance of 2.2 K ohm.
 // The laser SMB connector has an input impedance of 50 ohm.
-// --> This means that a the same resistor value have to be put in series between 
+// --> This means that a the same resistor value have to be put in series between
 // the pin and the connector on the laser.
 
 #define pinLT 4 // Laser Trigger pin
@@ -123,17 +81,17 @@ Below is the current version of the Arduino sketch:
 #define pinLED 13
 
 // Parameters:
-unsigned long delaytime=0; 
+unsigned long delaytime=0;
 unsigned long duration=5000;
 
 
 // We define what is INT and NOINT for the camera:
 #define INT HIGH
-#define NOINT LOW 
+#define NOINT LOW
 
-// We define what is LON and LOFF for the laser: 
+// We define what is LON and LOFF for the laser:
 #define LON HIGH
-#define LOFF LOW 
+#define LOFF LOW
 
 // Monitored pin state:
 volatile int state = NOINT;
@@ -144,7 +102,7 @@ volatile boolean pause=false;
 
 
 void setup()
-{ 
+{
   Serial.begin(115200);
   Serial.println("OpenSPIM ARDUSYNC> Connected!");
 
@@ -157,7 +115,7 @@ void setup()
   digitalWrite(pinLED, LOW);
   Serial.println("OpenSPIM ARDUSYNC> pins configured!");
 
-  //Attach the interrupts: 
+  //Attach the interrupts:
   // Interrupt 0 is on DIGITAL PIN 2!
   // Interrupt 1 is on DIGITAL PIN 3!
   // Arduino Mega has an additional four: numbers 2 (pin 21), 3 (pin 20), 4 (pin 19), and 5 (pin 18).
@@ -216,18 +174,18 @@ void delaymicro(long microseconds)
   if(microseconds>16383)
   {
     delay(microseconds/1000);
-    delayMicroseconds(microseconds%1000); 
+    delayMicroseconds(microseconds%1000);
   }
   else
   {
-    delayMicroseconds(microseconds); 
+    delayMicroseconds(microseconds);
   }
 }
 
 boolean messageStart(char id)
 {
   int i, serAva;                          // i is a counter, serAva hold number of serial available
-  char inputBytes [7]; 
+  char inputBytes [7];
   if (Serial.available()>=2)               // Check to see if there are any serial input
   {
     delay(5);                              // Delay for terminal to finish transmitted
@@ -237,9 +195,9 @@ boolean messageStart(char id)
     inputBytes[2] =  '\0';                 // Put NULL character at the end
     //Serial.println(inputBytes);
     if(inputBytes[0]==id && inputBytes[1]=='=')
-    { 
+    {
       return true;
-    } 
+    }
   }
   return false;
 }
@@ -271,4 +229,4 @@ long serReadInt(char id)
   else
     return -1;                           // Return -1 if there is no input
 }
-```
+</pre>

Beads.md

@@ -5,8 +5,7 @@ This page is about fluorescent beads, used as fiduciary markers for multi-view r
 ## Estapor Fluorescent Microspheres
 
   - [website](https://www.estapor.com/estapor/en/fluorescent_microspheres/fluorescent_microspheres/19.html)
-  - stock concentration for SPIM: 14 µl 0.5 µm beads in 14 ml medium
-    (sample dependent, e.g. PBS/T for fruit fly, E3 for zebrafish)
+  - stock concentration for SPIM: 14 µl 0.5 µm beads in 14 ml medium (sample dependent, e.g. PBS/T for fruit fly, E3 for zebrafish)
 
 ### Tips & tricks
 
@@ -18,7 +17,7 @@ This page is about fluorescent beads, used as fiduciary markers for multi-view r
   - diameter 0.5 µm
   - "green" emission (see spectra)
   - EX 488 nm
-  - appliations:
+  - applications:
       - fiduciary marker in "green" detection channel for bright "green" fluorescence
       - evaluation/adjustment of red-green overlay
 

Brightfield.md

@@ -1,7 +1,6 @@
 ---
 ---
-Strategies to implement a proper brightfield illumination in an
-OpenSPIM.
+Strategies to implement a proper brightfield illumination in an OpenSPIM.
 
 ## Michael Redd's solution
 
@@ -14,18 +13,10 @@ OpenSPIM.
 
 ### setup & wiring
 
-The arduino and light are powered by USB and are turned on and off by
-micro-manager and can be used as a brightfield channel in micromanager
-multi-dimensional acquisition window. The potentiometer and resistor
-determine the intensity of the light. The diode is fixed in place behind
-a collimating lens which fills the back aperture of a 10x immersion lens
-on axis with the sample and imaging lens. If your SPIM rig does not have
-a appropriate port and/or you do not have the 10x lens, one could focus
-the diode on the sample from above at an oblique angle. This may require
-a brighter light, but would probably work with the diode I am using.
-Light level can be dialed in by using different resistors and
-potentiometers.
+The Arduino and light are powered by USB and are turned on and off by micro-manager and can be used as a brightfield channel in micromanager multi-dimensional acquisition window. The potentiometer and resistor determine the intensity of the light. The diode is fixed in place behind a collimating lens which fills the back aperture of a 10x immersion lens on axis with the sample and imaging lens. If your SPIM rig does not have a appropriate port and/or you do not have the 10x lens, one could focus the diode on the sample from above at an oblique angle. This may require a brighter light, but would probably work with the diode I am using. Light level can be dialed in by using different resistors and potentiometers.
 
 by Michael Redd, Cell Imaging Core Facility, University of Utah
 
-<File:Redd> brightfield.png|setup <File:Redd> brightfield2.png|wiring
+{% include image src="Redd_brightfield.png" width="70%" caption="Setup" %}
+
+{% include image src="Redd_brightfield2.png" width="70%" caption="Wiring" %}