From e6aed7ec46ca873fb990e3b8d15edd026ce806e6 Mon Sep 17 00:00:00 2001
From: Patricia <patricialg@users.noreply.github.com>
Date: Tue, 8 Feb 2022 17:17:47 +0000
Subject: [PATCH 01/40] add sub-section for To-Do list

We created a cheat/To-Do list which is a summary of steps suggested in this SOP. Please, check you agree with the sections selected.
---
 sections/oxygen_introduction.md | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 9c2b3a3..95cc456 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -15,3 +15,29 @@ This standard operating procedure (SOP) document for dissolved oxygen (DO) aims
 |  Contros Hydroflash (1) |   |   | X |   |   |   | [Link](https://www.kongsberg.com/globalassets/maritime/km-products/product-documents/hydroflash-accurate-fast-and-versatile-oxygen-optode/Download) |
 
 (1)The advanced, optical sensor is based on the principle of fluorescence quenching. Contros are no longer in operation, the sensors cannot be calibrated so they are likely to become obsolete in the future. 
+
+## Summary of all steps recommended in this SOP.
+
+The most important steps described in this SOP can be summarised in this simple To-Do list:  
+
+**Pre-deployment/Deployment**
+1. Check that sensors are in good condition and you have selected the best option for the planned mission.
+    • BEST: Do two-point calibration (see section {numref}`Two_point_calibration_procedure,_optode_example`).
+2. Mount the sensor(s) (see section {numref}`Sensor_integration_with_gliders`). 
+3. Configure sensor for deployment (see section {numref}`Sensor_configuration_for_deployment`). Make sure your glider is configured to record phase with correct timings.
+4. Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil (see section {numref}`Storage_and_cleaning`).
+5. Do two-point calibration shortly before deployment (see section {numref}`Two_point_calibration_procedure,_optode_example`).
+6. In-situ reference measurements recommended to do, using hierarchy of decreasing quality:
+    • BEST: Optodes attached to a CTD (see section {numref}`Calibration_during_deployment/recovery_from_a ship_with_a_CTD_rosette_equipped_with_a_calibrated_oxygen_sensor`).
+    • BEST: multiple co-located CTD casts in well mixed waters (including Winkler samples at different depths) and in-air drift correction.
+    • GOOD: single point Winkler sample and CTD from nearby and no drift correction (see section {numref}`In_situ_intercomparison_during_deployment/recovery_from_a_small_boat`).
+    • OK: in-air calibration only (see section {numref}`In-air_calibration`).
+
+**Recovery** (Section {numref}`Post-recovery_operations_and_calibrations`).
+7. Keep sensor foil wet until finish in-situ reference mesurements (Point 9).
+8. Download data.
+9. In-situ reference measurements recommended to do, using hierarchy of decreasing quality as mentioned in Point 6.
+10. Clean and store the sensor.
+
+**DMQC** (Section {numref}`Delayed_Mode_Quality_Control`).
+11. Determine and correct optode lag

From 333a5b2f8f01731be87b51393d429a336260cc01 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 09:45:04 +0100
Subject: [PATCH 02/40] add (in-air-calibration)= handle

---
 sections/oxygen_mission_execution.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sections/oxygen_mission_execution.md b/sections/oxygen_mission_execution.md
index aaea2d0..1ad37ec 100644
--- a/sections/oxygen_mission_execution.md
+++ b/sections/oxygen_mission_execution.md
@@ -120,6 +120,7 @@ In regions with known oxygen concentrations i.e. within the core of the Peruvian
 For this glider can be parked at this depth to get a 0 calibration at the beginning and at the end of the deployment. 
 This can also be done by adding different depth/temperature levels if the anoxic layer is thick enough to cover different temperatures. i.e. further offshore where the OMZ is several 100 m thick.
 
+(in-air-calibration)=
 #### In-air calibration
 In-air calibration can be carried out if optodes are attached in a way that they reach out of the water when the glider is surfacing {cite}`NicholsonFeen2017` as done also for long float deployments {cite}`Bittig2018` 
 This can be valuable in particular if no 0 / 100 % lab calibration or CTD intercomparison is available as well as for long deployments. 

From 2a2b2f252255c3dc151ea4d4e7dac45eac25e757 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 09:46:34 +0100
Subject: [PATCH 03/40] add (dmqc)= handle

---
 sections/oxygen_dmqc.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sections/oxygen_dmqc.md b/sections/oxygen_dmqc.md
index 3fefa32..fef7879 100644
--- a/sections/oxygen_dmqc.md
+++ b/sections/oxygen_dmqc.md
@@ -1,3 +1,4 @@
+(dmqc)=
 # Delayed Mode Quality Control
 
 ## Calculation of oxygen variables

From 4ffa387d882a136c9c89a6988885df4c9a412075 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 09:48:52 +0100
Subject: [PATCH 04/40] correct {numref}`dmqc` reference

---
 sections/oxygen_introduction.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 95cc456..8ecdb0d 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -39,5 +39,5 @@ The most important steps described in this SOP can be summarised in this simple
 9. In-situ reference measurements recommended to do, using hierarchy of decreasing quality as mentioned in Point 6.
 10. Clean and store the sensor.
 
-**DMQC** (Section {numref}`Delayed_Mode_Quality_Control`).
+**DMQC** (Section {numref}`dmqc`).
 11. Determine and correct optode lag

From bf2356753ecfb15a280f8c4f8fe381fb94e9c360 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 09:53:17 +0100
Subject: [PATCH 05/40] add (post-recovery)= reference handle

---
 sections/oxygen_post_recovery.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sections/oxygen_post_recovery.md b/sections/oxygen_post_recovery.md
index 27dc5db..ff89408 100644
--- a/sections/oxygen_post_recovery.md
+++ b/sections/oxygen_post_recovery.md
@@ -1,3 +1,4 @@
+(post-recovery)=
 # Post-recovery operations and calibrations
 
 At first users should report that their mission is over to support(at)oceanobs.org

From deb9df174708328f52b7a0d6f6cd6b9febcaecd8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 09:54:01 +0100
Subject: [PATCH 06/40] reference post-recovery section

---
 sections/oxygen_introduction.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 8ecdb0d..5a8c00b 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -33,7 +33,7 @@ The most important steps described in this SOP can be summarised in this simple
     • GOOD: single point Winkler sample and CTD from nearby and no drift correction (see section {numref}`In_situ_intercomparison_during_deployment/recovery_from_a_small_boat`).
     • OK: in-air calibration only (see section {numref}`In-air_calibration`).
 
-**Recovery** (Section {numref}`Post-recovery_operations_and_calibrations`).
+**Recovery** (Section {numref}`post-recovery`).
 7. Keep sensor foil wet until finish in-situ reference mesurements (Point 9).
 8. Download data.
 9. In-situ reference measurements recommended to do, using hierarchy of decreasing quality as mentioned in Point 6.

From 22b1aad8c614b63b49c6e158243f43b4c21281c0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 09:56:38 +0100
Subject: [PATCH 07/40] correct {numref}`in-air-calibration` reference

---
 sections/oxygen_introduction.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 5a8c00b..429804a 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -31,7 +31,7 @@ The most important steps described in this SOP can be summarised in this simple
     • BEST: Optodes attached to a CTD (see section {numref}`Calibration_during_deployment/recovery_from_a ship_with_a_CTD_rosette_equipped_with_a_calibrated_oxygen_sensor`).
     • BEST: multiple co-located CTD casts in well mixed waters (including Winkler samples at different depths) and in-air drift correction.
     • GOOD: single point Winkler sample and CTD from nearby and no drift correction (see section {numref}`In_situ_intercomparison_during_deployment/recovery_from_a_small_boat`).
-    • OK: in-air calibration only (see section {numref}`In-air_calibration`).
+    • OK: in-air calibration only (see section {numref}`in-air-calibration`).
 
 **Recovery** (Section {numref}`post-recovery`).
 7. Keep sensor foil wet until finish in-situ reference mesurements (Point 9).

From 92b776693bfe6294ae59c40d2ffd0ce7df4e9df7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 09:58:38 +0100
Subject: [PATCH 08/40] fix: formatting

---
 sections/oxygen_introduction.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 429804a..3fae98d 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -31,13 +31,13 @@ The most important steps described in this SOP can be summarised in this simple
     • BEST: Optodes attached to a CTD (see section {numref}`Calibration_during_deployment/recovery_from_a ship_with_a_CTD_rosette_equipped_with_a_calibrated_oxygen_sensor`).
     • BEST: multiple co-located CTD casts in well mixed waters (including Winkler samples at different depths) and in-air drift correction.
     • GOOD: single point Winkler sample and CTD from nearby and no drift correction (see section {numref}`In_situ_intercomparison_during_deployment/recovery_from_a_small_boat`).
-    • OK: in-air calibration only (see section {numref}`in-air-calibration`).
+    • OK: in-air calibration only (see {numref}`in-air-calibration`).
 
-**Recovery** (Section {numref}`post-recovery`).
+**Recovery** ({numref}`post-recovery`).
 7. Keep sensor foil wet until finish in-situ reference mesurements (Point 9).
 8. Download data.
 9. In-situ reference measurements recommended to do, using hierarchy of decreasing quality as mentioned in Point 6.
 10. Clean and store the sensor.
 
-**DMQC** (Section {numref}`dmqc`).
+**DMQC** ({numref}`dmqc`).
 11. Determine and correct optode lag

From 3e00f1505a90b5b49b7e58b389aa2718b1290859 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 10:06:41 +0100
Subject: [PATCH 09/40] add deployment_ship_CTD reference handle

---
 sections/oxygen_introduction.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 3fae98d..cec95cc 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -28,7 +28,7 @@ The most important steps described in this SOP can be summarised in this simple
 4. Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil (see section {numref}`Storage_and_cleaning`).
 5. Do two-point calibration shortly before deployment (see section {numref}`Two_point_calibration_procedure,_optode_example`).
 6. In-situ reference measurements recommended to do, using hierarchy of decreasing quality:
-    • BEST: Optodes attached to a CTD (see section {numref}`Calibration_during_deployment/recovery_from_a ship_with_a_CTD_rosette_equipped_with_a_calibrated_oxygen_sensor`).
+    • BEST: Optodes attached to a CTD (see section {numref}`deployment_ship_CTD`).
     • BEST: multiple co-located CTD casts in well mixed waters (including Winkler samples at different depths) and in-air drift correction.
     • GOOD: single point Winkler sample and CTD from nearby and no drift correction (see section {numref}`In_situ_intercomparison_during_deployment/recovery_from_a_small_boat`).
     • OK: in-air calibration only (see {numref}`in-air-calibration`).

From d4a7fb28f15a18e143c4f82be1db90006e7f518c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 10:07:28 +0100
Subject: [PATCH 10/40] fix: formatting

remove the (see ... ) to keep it shorter
---
 sections/oxygen_introduction.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index cec95cc..dbdc5dd 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -26,12 +26,12 @@ The most important steps described in this SOP can be summarised in this simple
 2. Mount the sensor(s) (see section {numref}`Sensor_integration_with_gliders`). 
 3. Configure sensor for deployment (see section {numref}`Sensor_configuration_for_deployment`). Make sure your glider is configured to record phase with correct timings.
 4. Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil (see section {numref}`Storage_and_cleaning`).
-5. Do two-point calibration shortly before deployment (see section {numref}`Two_point_calibration_procedure,_optode_example`).
+5. Do two-point calibration shortly before deployment ({numref}`Two_point_calibration_procedure,_optode_example`).
 6. In-situ reference measurements recommended to do, using hierarchy of decreasing quality:
-    • BEST: Optodes attached to a CTD (see section {numref}`deployment_ship_CTD`).
+    • BEST: Optodes attached to a CTD ({numref}`deployment_ship_CTD`).
     • BEST: multiple co-located CTD casts in well mixed waters (including Winkler samples at different depths) and in-air drift correction.
     • GOOD: single point Winkler sample and CTD from nearby and no drift correction (see section {numref}`In_situ_intercomparison_during_deployment/recovery_from_a_small_boat`).
-    • OK: in-air calibration only (see {numref}`in-air-calibration`).
+    • OK: in-air calibration only ({numref}`in-air-calibration`).
 
 **Recovery** ({numref}`post-recovery`).
 7. Keep sensor foil wet until finish in-situ reference mesurements (Point 9).

From 8dda597af4a0414603be892c58b4655096f40a12 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 10:08:01 +0100
Subject: [PATCH 11/40] correct storage_and_cleaning handle

---
 sections/oxygen_introduction.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index dbdc5dd..2870268 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -25,7 +25,7 @@ The most important steps described in this SOP can be summarised in this simple
     • BEST: Do two-point calibration (see section {numref}`Two_point_calibration_procedure,_optode_example`).
 2. Mount the sensor(s) (see section {numref}`Sensor_integration_with_gliders`). 
 3. Configure sensor for deployment (see section {numref}`Sensor_configuration_for_deployment`). Make sure your glider is configured to record phase with correct timings.
-4. Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil (see section {numref}`Storage_and_cleaning`).
+4. Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil ({numref}`storage_and_cleaning`).
 5. Do two-point calibration shortly before deployment ({numref}`Two_point_calibration_procedure,_optode_example`).
 6. In-situ reference measurements recommended to do, using hierarchy of decreasing quality:
     • BEST: Optodes attached to a CTD ({numref}`deployment_ship_CTD`).

From 4f3b0e596205a80dde145fa79022a6aefb589622 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 10:08:36 +0100
Subject: [PATCH 12/40] add storage_and_cleaning handle

---
 sections/oxygen_pre_deployment.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sections/oxygen_pre_deployment.md b/sections/oxygen_pre_deployment.md
index 33bf30e..4ee861e 100644
--- a/sections/oxygen_pre_deployment.md
+++ b/sections/oxygen_pre_deployment.md
@@ -1,5 +1,6 @@
 # Pre-deployment operations and calibrations
 
+(storage_and_cleaning)=
 ## Storage and cleaning
 Optode foils typically drift more while in storage than while in use, the reasons for this are thought to be due to exposure to UV radiation and dry air {cite}`Bittig2018`, {cite}`Aanderaa2018`. 
 We recommend that all optodes should be stored away from the light (especially fluorescent lights), keep the foil humid and use the plastic caps provided with the sensor. Two-point calibration prior to deployment is always recommended.

From aa01570d9d76f90fd471daf59f57244fe84b723a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 10:15:15 +0100
Subject: [PATCH 13/40] correct two_point_calibration reference handle

---
 sections/oxygen_introduction.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 2870268..4399ce3 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -22,7 +22,7 @@ The most important steps described in this SOP can be summarised in this simple
 
 **Pre-deployment/Deployment**
 1. Check that sensors are in good condition and you have selected the best option for the planned mission.
-    • BEST: Do two-point calibration (see section {numref}`Two_point_calibration_procedure,_optode_example`).
+    • BEST: Do two-point calibration ({numref}`two_point_calibration`).
 2. Mount the sensor(s) (see section {numref}`Sensor_integration_with_gliders`). 
 3. Configure sensor for deployment (see section {numref}`Sensor_configuration_for_deployment`). Make sure your glider is configured to record phase with correct timings.
 4. Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil ({numref}`storage_and_cleaning`).

From c195e2e2df275ac986de82703b7b2c4be2026ad4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 10:16:00 +0100
Subject: [PATCH 14/40] add (two_point_calibration)= reference handle

---
 sections/oxygen_pre_deployment.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sections/oxygen_pre_deployment.md b/sections/oxygen_pre_deployment.md
index 4ee861e..1be0d71 100644
--- a/sections/oxygen_pre_deployment.md
+++ b/sections/oxygen_pre_deployment.md
@@ -57,6 +57,7 @@ You will need to leave the sensor logging outside in the free air for several ho
 ## Pre-deployment calibration
 Optodes and similar instruments generally drift more while in storage than in use. It is therefore essential that these instruments are recalibrated prior to glider deployment. This is necessary even if in-situ reference (Winkler) samples are taken during the deployment as they will not cover the full range of oxygen concentrations during the period of the mission. As the instrument drift manifests as an increasing offset from zero in addition to a reducing sensitivity, a two point calibration is required to rescale the optodes measuring range.
 
+(two_point_calibration)=
 ### Two point calibration procedure, optode example
 This protocol is recommended to do for at least two different temperatures, which cover the expected in-situ temperature range. 
 There are several possibilities in order to achieve this, some examples:

From 7457c6021ddf0d0ada3f640e499dd4dfefe662af Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 10:17:41 +0100
Subject: [PATCH 15/40] define (sensors_integration)= handle

---
 sections/oxygen_sensors_integration.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sections/oxygen_sensors_integration.md b/sections/oxygen_sensors_integration.md
index 1848349..8d0ab42 100644
--- a/sections/oxygen_sensors_integration.md
+++ b/sections/oxygen_sensors_integration.md
@@ -1,3 +1,4 @@
+(sensors_integration)=
 # Sensors and integrations 
 
 ## Oxygen sensors

From fe69c4144c14ea64a84bf2335ec3ced19920b264 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 10:18:34 +0100
Subject: [PATCH 16/40] reference (sensors_integration)= section

---
 sections/oxygen_introduction.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 4399ce3..31c0ad2 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -23,8 +23,8 @@ The most important steps described in this SOP can be summarised in this simple
 **Pre-deployment/Deployment**
 1. Check that sensors are in good condition and you have selected the best option for the planned mission.
     • BEST: Do two-point calibration ({numref}`two_point_calibration`).
-2. Mount the sensor(s) (see section {numref}`Sensor_integration_with_gliders`). 
-3. Configure sensor for deployment (see section {numref}`Sensor_configuration_for_deployment`). Make sure your glider is configured to record phase with correct timings.
+2. Mount the sensor(s) ({numref}`sensors_integration`). 
+3. Configure sensor for deployment ({numref}`Sensor_configuration_for_deployment`). Make sure your glider is configured to record phase with correct timings.
 4. Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil ({numref}`storage_and_cleaning`).
 5. Do two-point calibration shortly before deployment ({numref}`Two_point_calibration_procedure,_optode_example`).
 6. In-situ reference measurements recommended to do, using hierarchy of decreasing quality:

From 79c50f05d6585f4e5eb430c5aedf27f50c0d0d4c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 10:45:30 +0100
Subject: [PATCH 17/40] update "sensor_configuration" handle

---
 sections/oxygen_introduction.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 31c0ad2..06390d4 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -24,7 +24,7 @@ The most important steps described in this SOP can be summarised in this simple
 1. Check that sensors are in good condition and you have selected the best option for the planned mission.
     • BEST: Do two-point calibration ({numref}`two_point_calibration`).
 2. Mount the sensor(s) ({numref}`sensors_integration`). 
-3. Configure sensor for deployment ({numref}`Sensor_configuration_for_deployment`). Make sure your glider is configured to record phase with correct timings.
+3. Configure sensor for deployment ({numref}`sensor_configuration`). Make sure your glider is configured to record phase with correct timings.
 4. Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil ({numref}`storage_and_cleaning`).
 5. Do two-point calibration shortly before deployment ({numref}`Two_point_calibration_procedure,_optode_example`).
 6. In-situ reference measurements recommended to do, using hierarchy of decreasing quality:

From 3e445f6189101e459d2b97e39ead944682ee537e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 10:46:01 +0100
Subject: [PATCH 18/40] add sensor_configuration reference handle

---
 sections/oxygen_pre_deployment.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sections/oxygen_pre_deployment.md b/sections/oxygen_pre_deployment.md
index 1be0d71..43d1e97 100644
--- a/sections/oxygen_pre_deployment.md
+++ b/sections/oxygen_pre_deployment.md
@@ -21,6 +21,7 @@ After recovery the sensor has to be cleaned to remove any biofouling. The follow
 
 *NOTE: Don’t change the foil unless it is physically damaged.* 
 
+(sensor_configuration)=
 ## Sensor configuration for deployment
 Salinity configuration: 0 PSU. 
 For optode sensors: when there is a small variation in salinity (less than 1 g/kg), it can be set to the mid value avoiding the need of salinity compensation. 

From 699f111e413836d3e01befdd663d43018291f127 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 11:05:51 +0100
Subject: [PATCH 19/40] fix: formatting

---
 sections/oxygen_introduction.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 06390d4..f62c0df 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -33,7 +33,7 @@ The most important steps described in this SOP can be summarised in this simple
     • GOOD: single point Winkler sample and CTD from nearby and no drift correction (see section {numref}`In_situ_intercomparison_during_deployment/recovery_from_a_small_boat`).
     • OK: in-air calibration only ({numref}`in-air-calibration`).
 
-**Recovery** ({numref}`post-recovery`).
+**Recovery** ({numref}`post-recovery`)
 7. Keep sensor foil wet until finish in-situ reference mesurements (Point 9).
 8. Download data.
 9. In-situ reference measurements recommended to do, using hierarchy of decreasing quality as mentioned in Point 6.

From 5592677da8abc2aa45c6623623c28e410415b09c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 11:16:08 +0100
Subject: [PATCH 20/40] correct `two_point_calibration` reference

---
 sections/oxygen_introduction.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index f62c0df..1f9d44b 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -26,7 +26,7 @@ The most important steps described in this SOP can be summarised in this simple
 2. Mount the sensor(s) ({numref}`sensors_integration`). 
 3. Configure sensor for deployment ({numref}`sensor_configuration`). Make sure your glider is configured to record phase with correct timings.
 4. Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil ({numref}`storage_and_cleaning`).
-5. Do two-point calibration shortly before deployment ({numref}`Two_point_calibration_procedure,_optode_example`).
+5. Do two-point calibration shortly before deployment ({numref}`two_point_calibration`).
 6. In-situ reference measurements recommended to do, using hierarchy of decreasing quality:
     • BEST: Optodes attached to a CTD ({numref}`deployment_ship_CTD`).
     • BEST: multiple co-located CTD casts in well mixed waters (including Winkler samples at different depths) and in-air drift correction.

From 9f73ec2396a6da55b281297bdf7f68dc9760569a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 11:22:28 +0100
Subject: [PATCH 21/40] correct deployment_small_boat handle

Also fixed some formatting
---
 sections/oxygen_introduction.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 1f9d44b..9db930a 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -22,16 +22,16 @@ The most important steps described in this SOP can be summarised in this simple
 
 **Pre-deployment/Deployment**
 1. Check that sensors are in good condition and you have selected the best option for the planned mission.
-    • BEST: Do two-point calibration ({numref}`two_point_calibration`).
+- BEST: Do two-point calibration ({numref}`two_point_calibration`).
 2. Mount the sensor(s) ({numref}`sensors_integration`). 
 3. Configure sensor for deployment ({numref}`sensor_configuration`). Make sure your glider is configured to record phase with correct timings.
 4. Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil ({numref}`storage_and_cleaning`).
 5. Do two-point calibration shortly before deployment ({numref}`two_point_calibration`).
 6. In-situ reference measurements recommended to do, using hierarchy of decreasing quality:
-    • BEST: Optodes attached to a CTD ({numref}`deployment_ship_CTD`).
-    • BEST: multiple co-located CTD casts in well mixed waters (including Winkler samples at different depths) and in-air drift correction.
-    • GOOD: single point Winkler sample and CTD from nearby and no drift correction (see section {numref}`In_situ_intercomparison_during_deployment/recovery_from_a_small_boat`).
-    • OK: in-air calibration only ({numref}`in-air-calibration`).
+- BEST: Optodes attached to a CTD ({numref}`deployment_ship_CTD`).
+- BEST: multiple co-located CTD casts in well mixed waters (including Winkler samples at different depths) and in-air drift correction.
+- GOOD: single point Winkler sample and CTD from nearby and no drift correction (see section {numref}`deployment_small_boat`).
+- OK: in-air calibration only ({numref}`in-air-calibration`).
 
 **Recovery** ({numref}`post-recovery`)
 7. Keep sensor foil wet until finish in-situ reference mesurements (Point 9).

From 7dacd01944a486c9684c7cbc16f70ca649ba5906 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 11:25:37 +0100
Subject: [PATCH 22/40] update title and section description

---
 sections/oxygen_introduction.md | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 9db930a..63ed667 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -16,9 +16,11 @@ This standard operating procedure (SOP) document for dissolved oxygen (DO) aims
 
 (1)The advanced, optical sensor is based on the principle of fluorescence quenching. Contros are no longer in operation, the sensors cannot be calibrated so they are likely to become obsolete in the future. 
 
-## Summary of all steps recommended in this SOP.
+## Overview cheat sheet
 
-The most important steps described in this SOP can be summarised in this simple To-Do list:  
+The most important actions to be taken are summarised in this simple cheat sheet below.
+This short summary allows the reader check under time pressure whether key points are taken into account prior to deployment.
+We recommend to read each chapter in detail to ensure best quality data.
 
 **Pre-deployment/Deployment**
 1. Check that sensors are in good condition and you have selected the best option for the planned mission.

From bea2ccea9244b1c48ac40ad821b517f87935778f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 11:35:58 +0100
Subject: [PATCH 23/40] fix: formatting

---
 sections/oxygen_introduction.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 63ed667..80a0cc7 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -24,16 +24,16 @@ We recommend to read each chapter in detail to ensure best quality data.
 
 **Pre-deployment/Deployment**
 1. Check that sensors are in good condition and you have selected the best option for the planned mission.
-- BEST: Do two-point calibration ({numref}`two_point_calibration`).
+  - BEST: Do two-point calibration ({numref}`two_point_calibration`).
 2. Mount the sensor(s) ({numref}`sensors_integration`). 
 3. Configure sensor for deployment ({numref}`sensor_configuration`). Make sure your glider is configured to record phase with correct timings.
 4. Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil ({numref}`storage_and_cleaning`).
 5. Do two-point calibration shortly before deployment ({numref}`two_point_calibration`).
 6. In-situ reference measurements recommended to do, using hierarchy of decreasing quality:
-- BEST: Optodes attached to a CTD ({numref}`deployment_ship_CTD`).
-- BEST: multiple co-located CTD casts in well mixed waters (including Winkler samples at different depths) and in-air drift correction.
-- GOOD: single point Winkler sample and CTD from nearby and no drift correction (see section {numref}`deployment_small_boat`).
-- OK: in-air calibration only ({numref}`in-air-calibration`).
+  - BEST: Optodes attached to a CTD ({numref}`deployment_ship_CTD`).
+  - BEST: multiple co-located CTD casts in well mixed waters (including Winkler samples at different depths) and in-air drift correction.
+  - GOOD: single point Winkler sample and CTD from nearby and no drift correction (see section {numref}`deployment_small_boat`).
+  - OK: in-air calibration only ({numref}`in-air-calibration`).
 
 **Recovery** ({numref}`post-recovery`)
 7. Keep sensor foil wet until finish in-situ reference mesurements (Point 9).

From 33d1985de8ace7f980caea0a2e557f4f14309ef2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 11:41:38 +0100
Subject: [PATCH 24/40] fix: try to correct numbering

---
 sections/oxygen_introduction.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 80a0cc7..eea0fe7 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -25,6 +25,7 @@ We recommend to read each chapter in detail to ensure best quality data.
 **Pre-deployment/Deployment**
 1. Check that sensors are in good condition and you have selected the best option for the planned mission.
   - BEST: Do two-point calibration ({numref}`two_point_calibration`).
+  
 2. Mount the sensor(s) ({numref}`sensors_integration`). 
 3. Configure sensor for deployment ({numref}`sensor_configuration`). Make sure your glider is configured to record phase with correct timings.
 4. Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil ({numref}`storage_and_cleaning`).

From 6fe38eaf0b9021527798feda481c9d1bc6326277 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 11:57:39 +0100
Subject: [PATCH 25/40] add spaces

---
 sections/oxygen_introduction.md | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index eea0fe7..8449c5b 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -26,21 +26,21 @@ We recommend to read each chapter in detail to ensure best quality data.
 1. Check that sensors are in good condition and you have selected the best option for the planned mission.
   - BEST: Do two-point calibration ({numref}`two_point_calibration`).
   
-2. Mount the sensor(s) ({numref}`sensors_integration`). 
-3. Configure sensor for deployment ({numref}`sensor_configuration`). Make sure your glider is configured to record phase with correct timings.
-4. Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil ({numref}`storage_and_cleaning`).
-5. Do two-point calibration shortly before deployment ({numref}`two_point_calibration`).
+2. Mount the sensor(s) ({numref}`sensors_integration`).   
+3. Configure sensor for deployment ({numref}`sensor_configuration`). Make sure your glider is configured to record phase with correct timings.  
+4. Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil ({numref}`storage_and_cleaning`).  
+5. Do two-point calibration shortly before deployment ({numref}`two_point_calibration`).  
 6. In-situ reference measurements recommended to do, using hierarchy of decreasing quality:
-  - BEST: Optodes attached to a CTD ({numref}`deployment_ship_CTD`).
+  - BEST: Optodes attached to a CTD ({numref}`deployment_ship_CTD`). 
   - BEST: multiple co-located CTD casts in well mixed waters (including Winkler samples at different depths) and in-air drift correction.
   - GOOD: single point Winkler sample and CTD from nearby and no drift correction (see section {numref}`deployment_small_boat`).
   - OK: in-air calibration only ({numref}`in-air-calibration`).
 
 **Recovery** ({numref}`post-recovery`)
-7. Keep sensor foil wet until finish in-situ reference mesurements (Point 9).
-8. Download data.
-9. In-situ reference measurements recommended to do, using hierarchy of decreasing quality as mentioned in Point 6.
-10. Clean and store the sensor.
+7. Keep sensor foil wet until finish in-situ reference mesurements (Point 9).  
+8. Download data.  
+9. In-situ reference measurements recommended to do, using hierarchy of decreasing quality as mentioned in Point 6.  
+10. Clean and store the sensor.  
 
 **DMQC** ({numref}`dmqc`).
-11. Determine and correct optode lag
+11. Determine and correct optode lag. 

From d4eca6de9e8ed5a5ceed6da0dc8a0bc1301d47d3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 12:01:41 +0100
Subject: [PATCH 26/40] tryfix: check spaces to get good numbering

---
 sections/oxygen_introduction.md | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 8449c5b..683e799 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -17,15 +17,13 @@ This standard operating procedure (SOP) document for dissolved oxygen (DO) aims
 (1)The advanced, optical sensor is based on the principle of fluorescence quenching. Contros are no longer in operation, the sensors cannot be calibrated so they are likely to become obsolete in the future. 
 
 ## Overview cheat sheet
-
 The most important actions to be taken are summarised in this simple cheat sheet below.
 This short summary allows the reader check under time pressure whether key points are taken into account prior to deployment.
 We recommend to read each chapter in detail to ensure best quality data.
 
 **Pre-deployment/Deployment**
 1. Check that sensors are in good condition and you have selected the best option for the planned mission.
-  - BEST: Do two-point calibration ({numref}`two_point_calibration`).
-  
+- BEST: Do two-point calibration ({numref}`two_point_calibration`).
 2. Mount the sensor(s) ({numref}`sensors_integration`).   
 3. Configure sensor for deployment ({numref}`sensor_configuration`). Make sure your glider is configured to record phase with correct timings.  
 4. Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil ({numref}`storage_and_cleaning`).  

From d2a99f116cfc86f371600889c6639753a64402e4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 12:06:40 +0100
Subject: [PATCH 27/40] test spaces

---
 sections/oxygen_introduction.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 683e799..05cca93 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -22,8 +22,8 @@ This short summary allows the reader check under time pressure whether key point
 We recommend to read each chapter in detail to ensure best quality data.
 
 **Pre-deployment/Deployment**
-1. Check that sensors are in good condition and you have selected the best option for the planned mission.
-- BEST: Do two-point calibration ({numref}`two_point_calibration`).
+1. Check that sensors are in good condition and you have selected the best option for the planned mission.  
+- BEST: Do two-point calibration ({numref}`two_point_calibration`).  
 2. Mount the sensor(s) ({numref}`sensors_integration`).   
 3. Configure sensor for deployment ({numref}`sensor_configuration`). Make sure your glider is configured to record phase with correct timings.  
 4. Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil ({numref}`storage_and_cleaning`).  

From 1c843b0bdb2f35943f439129773ad7e922bca278 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 12:10:56 +0100
Subject: [PATCH 28/40] work around: using (1) for list

the list with 1.
break.
2. etc does not work so I try (1)
---
 sections/oxygen_introduction.md | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 05cca93..cf83a41 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -14,7 +14,7 @@ This standard operating procedure (SOP) document for dissolved oxygen (DO) aims
 |  RBRcoda T.ODO |   |   |   |   | X |   | [Link](https://rbr-global.com/products/sensors/rbrcoda-odo) |
 |  Contros Hydroflash (1) |   |   | X |   |   |   | [Link](https://www.kongsberg.com/globalassets/maritime/km-products/product-documents/hydroflash-accurate-fast-and-versatile-oxygen-optode/Download) |
 
-(1)The advanced, optical sensor is based on the principle of fluorescence quenching. Contros are no longer in operation, the sensors cannot be calibrated so they are likely to become obsolete in the future. 
+(1) The advanced, optical sensor is based on the principle of fluorescence quenching. Contros are no longer in operation, the sensors cannot be calibrated so they are likely to become obsolete in the future. 
 
 ## Overview cheat sheet
 The most important actions to be taken are summarised in this simple cheat sheet below.
@@ -22,23 +22,23 @@ This short summary allows the reader check under time pressure whether key point
 We recommend to read each chapter in detail to ensure best quality data.
 
 **Pre-deployment/Deployment**
-1. Check that sensors are in good condition and you have selected the best option for the planned mission.  
+(1) Check that sensors are in good condition and you have selected the best option for the planned mission.  
 - BEST: Do two-point calibration ({numref}`two_point_calibration`).  
-2. Mount the sensor(s) ({numref}`sensors_integration`).   
-3. Configure sensor for deployment ({numref}`sensor_configuration`). Make sure your glider is configured to record phase with correct timings.  
-4. Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil ({numref}`storage_and_cleaning`).  
-5. Do two-point calibration shortly before deployment ({numref}`two_point_calibration`).  
-6. In-situ reference measurements recommended to do, using hierarchy of decreasing quality:
+(2) Mount the sensor(s) ({numref}`sensors_integration`).   
+(3) Configure sensor for deployment ({numref}`sensor_configuration`). Make sure your glider is configured to record phase with correct timings.  
+(4) Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil ({numref}`storage_and_cleaning`).  
+(5) Do two-point calibration shortly before deployment ({numref}`two_point_calibration`).  
+(6) In-situ reference measurements recommended to do, using hierarchy of decreasing quality:
   - BEST: Optodes attached to a CTD ({numref}`deployment_ship_CTD`). 
   - BEST: multiple co-located CTD casts in well mixed waters (including Winkler samples at different depths) and in-air drift correction.
   - GOOD: single point Winkler sample and CTD from nearby and no drift correction (see section {numref}`deployment_small_boat`).
   - OK: in-air calibration only ({numref}`in-air-calibration`).
 
 **Recovery** ({numref}`post-recovery`)
-7. Keep sensor foil wet until finish in-situ reference mesurements (Point 9).  
-8. Download data.  
-9. In-situ reference measurements recommended to do, using hierarchy of decreasing quality as mentioned in Point 6.  
-10. Clean and store the sensor.  
+(7) Keep sensor foil wet until finish in-situ reference mesurements (Point 9).  
+(8) Download data.  
+(9) In-situ reference measurements recommended to do, using hierarchy of decreasing quality as mentioned in Point 6.  
+(10) Clean and store the sensor.  
 
 **DMQC** ({numref}`dmqc`).
-11. Determine and correct optode lag. 
+(11) Determine and correct optode lag. 

From d9e97b75ab69d6907e2d4901d4f181b6ccc46c31 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 12:14:13 +0100
Subject: [PATCH 29/40] fix: formatting

---
 sections/oxygen_introduction.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index cf83a41..2a71119 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -21,9 +21,9 @@ The most important actions to be taken are summarised in this simple cheat sheet
 This short summary allows the reader check under time pressure whether key points are taken into account prior to deployment.
 We recommend to read each chapter in detail to ensure best quality data.
 
-**Pre-deployment/Deployment**
+**Pre-deployment/Deployment** 
 (1) Check that sensors are in good condition and you have selected the best option for the planned mission.  
-- BEST: Do two-point calibration ({numref}`two_point_calibration`).  
+  - BEST: Do two-point calibration ({numref}`two_point_calibration`).  
 (2) Mount the sensor(s) ({numref}`sensors_integration`).   
 (3) Configure sensor for deployment ({numref}`sensor_configuration`). Make sure your glider is configured to record phase with correct timings.  
 (4) Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil ({numref}`storage_and_cleaning`).  
@@ -34,7 +34,7 @@ We recommend to read each chapter in detail to ensure best quality data.
   - GOOD: single point Winkler sample and CTD from nearby and no drift correction (see section {numref}`deployment_small_boat`).
   - OK: in-air calibration only ({numref}`in-air-calibration`).
 
-**Recovery** ({numref}`post-recovery`)
+**Recovery** ({numref}`post-recovery`)  
 (7) Keep sensor foil wet until finish in-situ reference mesurements (Point 9).  
 (8) Download data.  
 (9) In-situ reference measurements recommended to do, using hierarchy of decreasing quality as mentioned in Point 6.  

From be1b69ace66b37dea5474fbaf474b2ffff33707b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 12:18:20 +0100
Subject: [PATCH 30/40] fix: formatting

---
 sections/oxygen_introduction.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 2a71119..64b8288 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -21,10 +21,10 @@ The most important actions to be taken are summarised in this simple cheat sheet
 This short summary allows the reader check under time pressure whether key points are taken into account prior to deployment.
 We recommend to read each chapter in detail to ensure best quality data.
 
-**Pre-deployment/Deployment** 
+**Pre-deployment/Deployment**  
 (1) Check that sensors are in good condition and you have selected the best option for the planned mission.  
   - BEST: Do two-point calibration ({numref}`two_point_calibration`).  
-(2) Mount the sensor(s) ({numref}`sensors_integration`).   
+(2) Mount the sensor(s) ({numref}`sensors_integration`).  
 (3) Configure sensor for deployment ({numref}`sensor_configuration`). Make sure your glider is configured to record phase with correct timings.  
 (4) Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil ({numref}`storage_and_cleaning`).  
 (5) Do two-point calibration shortly before deployment ({numref}`two_point_calibration`).  
@@ -40,5 +40,5 @@ We recommend to read each chapter in detail to ensure best quality data.
 (9) In-situ reference measurements recommended to do, using hierarchy of decreasing quality as mentioned in Point 6.  
 (10) Clean and store the sensor.  
 
-**DMQC** ({numref}`dmqc`).
+**DMQC** ({numref}`dmqc`)  
 (11) Determine and correct optode lag. 

From 216da67e31d8108957b6adb6eddbb490552bc82f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 12:22:07 +0100
Subject: [PATCH 31/40] fix: formatting

---
 sections/oxygen_introduction.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 64b8288..c497c61 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -24,6 +24,7 @@ We recommend to read each chapter in detail to ensure best quality data.
 **Pre-deployment/Deployment**  
 (1) Check that sensors are in good condition and you have selected the best option for the planned mission.  
   - BEST: Do two-point calibration ({numref}`two_point_calibration`).  
+ 
 (2) Mount the sensor(s) ({numref}`sensors_integration`).  
 (3) Configure sensor for deployment ({numref}`sensor_configuration`). Make sure your glider is configured to record phase with correct timings.  
 (4) Keep sensor foil wet at least 8 hours before deployment. If it cannot be kept submerged in water, have a wet sponge covering the foil ({numref}`storage_and_cleaning`).  

From 23bddb528177646bdd1799f8468db15f57526d31 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 12:28:31 +0100
Subject: [PATCH 32/40] organising: cheat sheet before table

I also added a subsection title to the table
---
 sections/oxygen_introduction.md | 30 ++++++++++++++++--------------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index c497c61..a1d914c 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -2,20 +2,6 @@
 
 This standard operating procedure (SOP) document for dissolved oxygen (DO) aims to guide the user through the steps necessary to collect good quality dissolved oxygen data using ocean gliders for both real time and post deployment data streams.
 
-*Table 1: List of the known sensor/glider combinations. We aim to cover all combinations in this document.*
-
-| Sensor / Glider  |  Slocum |  Autosub/ ALR (NOC) |  Seaglider | Deepglider  |  SeaExplorer |  Spray |  Information |
-|---|---|---|---|---|---|---|---|
-| Aanderaa 3835, 4330, 4330F, 4831, 4831F and 5013 optodes  | X |   | X | X |   |   | [Link](https://www.aanderaa.com/productsdetail.php?Oxygen-Optodes-2) |
-| RINKO-II  | X |   |   |   |   |  | [Link](https://www.jfe-advantech.co.jp/eng/ocean/rinko/rinko22d.html) |
-| RINKO- AROD FT  |   |   |   |   | X |   | [Link](https://www.jfe-advantech.co.jp/eng/ocean/rinko/rinko-ft.html) |
-| SBE 43 and 43F  |   | X | X |   | X |   | [Link](https://www.seabird.com/sbe-43-dissolved-oxygen-sensor-with-titanium-housing-mcbh-connector-0-5-mil-profiling-membrane-standard-43-plenum/product?id=54627923854) |
-| SBE 63  |   |   |   |   |   | X | [Link](https://www.seabird.com/oxygen-sensors/sbe-63-optical-dissolved-oxygen-sensor/family?productCategoryId=54627869933) |
-|  RBRcoda T.ODO |   |   |   |   | X |   | [Link](https://rbr-global.com/products/sensors/rbrcoda-odo) |
-|  Contros Hydroflash (1) |   |   | X |   |   |   | [Link](https://www.kongsberg.com/globalassets/maritime/km-products/product-documents/hydroflash-accurate-fast-and-versatile-oxygen-optode/Download) |
-
-(1) The advanced, optical sensor is based on the principle of fluorescence quenching. Contros are no longer in operation, the sensors cannot be calibrated so they are likely to become obsolete in the future. 
-
 ## Overview cheat sheet
 The most important actions to be taken are summarised in this simple cheat sheet below.
 This short summary allows the reader check under time pressure whether key points are taken into account prior to deployment.
@@ -43,3 +29,19 @@ We recommend to read each chapter in detail to ensure best quality data.
 
 **DMQC** ({numref}`dmqc`)  
 (11) Determine and correct optode lag. 
+
+## Overivew sensor glider combinations
+
+*Table 1: List of the known sensor/glider combinations. We aim to cover all combinations in this document.*
+
+| Sensor / Glider  |  Slocum |  Autosub/ ALR (NOC) |  Seaglider | Deepglider  |  SeaExplorer |  Spray |  Information |
+|---|---|---|---|---|---|---|---|
+| Aanderaa 3835, 4330, 4330F, 4831, 4831F and 5013 optodes  | X |   | X | X |   |   | [Link](https://www.aanderaa.com/productsdetail.php?Oxygen-Optodes-2) |
+| RINKO-II  | X |   |   |   |   |  | [Link](https://www.jfe-advantech.co.jp/eng/ocean/rinko/rinko22d.html) |
+| RINKO- AROD FT  |   |   |   |   | X |   | [Link](https://www.jfe-advantech.co.jp/eng/ocean/rinko/rinko-ft.html) |
+| SBE 43 and 43F  |   | X | X |   | X |   | [Link](https://www.seabird.com/sbe-43-dissolved-oxygen-sensor-with-titanium-housing-mcbh-connector-0-5-mil-profiling-membrane-standard-43-plenum/product?id=54627923854) |
+| SBE 63  |   |   |   |   |   | X | [Link](https://www.seabird.com/oxygen-sensors/sbe-63-optical-dissolved-oxygen-sensor/family?productCategoryId=54627869933) |
+|  RBRcoda T.ODO |   |   |   |   | X |   | [Link](https://rbr-global.com/products/sensors/rbrcoda-odo) |
+|  Contros Hydroflash (1) |   |   | X |   |   |   | [Link](https://www.kongsberg.com/globalassets/maritime/km-products/product-documents/hydroflash-accurate-fast-and-versatile-oxygen-optode/Download) |
+
+(1) The advanced, optical sensor is based on the principle of fluorescence quenching. Contros are no longer in operation, the sensors cannot be calibrated so they are likely to become obsolete in the future. 

From db0e3d9269a82963dca314a20b438b6be1d4f3ae Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 12:38:30 +0100
Subject: [PATCH 33/40] add mission-execution

---
 sections/oxygen_introduction.md | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index a1d914c..1e3a80a 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -21,16 +21,19 @@ We recommend to read each chapter in detail to ensure best quality data.
   - GOOD: single point Winkler sample and CTD from nearby and no drift correction (see section {numref}`deployment_small_boat`).
   - OK: in-air calibration only ({numref}`in-air-calibration`).
 
+**Mission** ({numref}`mission-execution`)  
+(7) Ensure data stream is set up and relevant metadata is sent to allow real time data corrections.
+
 **Recovery** ({numref}`post-recovery`)  
-(7) Keep sensor foil wet until finish in-situ reference mesurements (Point 9).  
-(8) Download data.  
-(9) In-situ reference measurements recommended to do, using hierarchy of decreasing quality as mentioned in Point 6.  
-(10) Clean and store the sensor.  
+(8) Keep sensor foil wet until finish in-situ reference mesurements (Point 9).  
+(9) Download data.  
+(10) In-situ reference measurements recommended to do, using hierarchy of decreasing quality as mentioned in Point 6.  
+(11) Clean and store the sensor.  
 
 **DMQC** ({numref}`dmqc`)  
-(11) Determine and correct optode lag. 
+(12) Determine and correct optode lag. 
 
-## Overivew sensor glider combinations
+## Overview sensor glider combinations
 
 *Table 1: List of the known sensor/glider combinations. We aim to cover all combinations in this document.*
 

From b47a4152e5e7d88b8eb94feef3564ae987c04b7f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 12:39:05 +0100
Subject: [PATCH 34/40] add (mission-execution)= handle for referencing

---
 sections/oxygen_mission_execution.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sections/oxygen_mission_execution.md b/sections/oxygen_mission_execution.md
index 1ad37ec..07a548d 100644
--- a/sections/oxygen_mission_execution.md
+++ b/sections/oxygen_mission_execution.md
@@ -1,3 +1,4 @@
+(mission-execution)=
 # Missions execution
 
 This section covers the activities of those deploying and recovering the gliders in the field in addition to best practices for glider pilots.

From 1b4f0f4ddd904ed7f40f44e373a37dc47b07d594 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 12:45:08 +0100
Subject: [PATCH 35/40] add (rtqc)= handle for referencing

---
 sections/oxygen_rtqc.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sections/oxygen_rtqc.md b/sections/oxygen_rtqc.md
index 0ab49dc..7e37067 100644
--- a/sections/oxygen_rtqc.md
+++ b/sections/oxygen_rtqc.md
@@ -1,3 +1,4 @@
+(rtqc)=
 # Required Metadata, Real Time Data Processing & Quality Control
 
 ## Required Metadata and Real Time Data Processing

From d16ac9fe9dc637868095f4e0b371d6ac419d4dd7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 12:46:39 +0100
Subject: [PATCH 36/40] add `rtqc` reference

---
 sections/oxygen_introduction.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 1e3a80a..15f5242 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -21,8 +21,8 @@ We recommend to read each chapter in detail to ensure best quality data.
   - GOOD: single point Winkler sample and CTD from nearby and no drift correction (see section {numref}`deployment_small_boat`).
   - OK: in-air calibration only ({numref}`in-air-calibration`).
 
-**Mission** ({numref}`mission-execution`)  
-(7) Ensure data stream is set up and relevant metadata is sent to allow real time data corrections.
+**Mission and Real Time data flow** ({numref}`mission-execution`)  
+(7) Ensure data stream is set up correctly including relevant metadata is sent to allow real time data corrections ({numref}`rtqc`).
 
 **Recovery** ({numref}`post-recovery`)  
 (8) Keep sensor foil wet until finish in-situ reference mesurements (Point 9).  

From 6b85186e679c3444fec67158a05d452e7a91fd9e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 12:47:57 +0100
Subject: [PATCH 37/40] remove links to points

This will lead to errors if we modify the list
---
 sections/oxygen_introduction.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 15f5242..239be45 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -25,9 +25,9 @@ We recommend to read each chapter in detail to ensure best quality data.
 (7) Ensure data stream is set up correctly including relevant metadata is sent to allow real time data corrections ({numref}`rtqc`).
 
 **Recovery** ({numref}`post-recovery`)  
-(8) Keep sensor foil wet until finish in-situ reference mesurements (Point 9).  
+(8) Keep sensor foil wet until finish in-situ reference mesurements.  
 (9) Download data.  
-(10) In-situ reference measurements recommended to do, using hierarchy of decreasing quality as mentioned in Point 6.  
+(10) In-situ reference measurements recommended to do, using hierarchy of decreasing quality as mentioned above.  
 (11) Clean and store the sensor.  
 
 **DMQC** ({numref}`dmqc`)  

From 62748baeabeacb98315abb2ff83ddc056dd207f3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 12:49:24 +0100
Subject: [PATCH 38/40] fix: referencing

---
 sections/oxygen_introduction.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 239be45..7bd2c8d 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -25,7 +25,7 @@ We recommend to read each chapter in detail to ensure best quality data.
 (7) Ensure data stream is set up correctly including relevant metadata is sent to allow real time data corrections ({numref}`rtqc`).
 
 **Recovery** ({numref}`post-recovery`)  
-(8) Keep sensor foil wet until finish in-situ reference mesurements.  
+(8) Keep sensor foil wet until finish post deployment in-situ reference measurements.  
 (9) Download data.  
 (10) In-situ reference measurements recommended to do, using hierarchy of decreasing quality as mentioned above.  
 (11) Clean and store the sensor.  

From 777a3c4d54dd7a2e9360734cf7c152c484d4af8f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 12:56:36 +0100
Subject: [PATCH 39/40] add data-sharing

---
 sections/oxygen_introduction.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/sections/oxygen_introduction.md b/sections/oxygen_introduction.md
index 7bd2c8d..cd4c661 100644
--- a/sections/oxygen_introduction.md
+++ b/sections/oxygen_introduction.md
@@ -33,6 +33,9 @@ We recommend to read each chapter in detail to ensure best quality data.
 **DMQC** ({numref}`dmqc`)  
 (12) Determine and correct optode lag. 
 
+**Data sharing** ({numref}`data-sharing`)  
+(13) Share high quality data in public open access archives.
+
 ## Overview sensor glider combinations
 
 *Table 1: List of the known sensor/glider combinations. We aim to cover all combinations in this document.*

From 65930ba3fb0b0b40475ce3721855429880fa4305 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20Thomsen?=
 <32633545+soerenthomsen@users.noreply.github.com>
Date: Wed, 9 Feb 2022 12:57:02 +0100
Subject: [PATCH 40/40] add data-sharing handle for referencing

---
 sections/data_sharing.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sections/data_sharing.md b/sections/data_sharing.md
index 7ae6782..1b74539 100644
--- a/sections/data_sharing.md
+++ b/sections/data_sharing.md
@@ -1,3 +1,4 @@
+(data-sharing)=
 # Data sharing
 
 OceanGliders strongly encourages all glider operators to share their data to the public and provide open access both in real time and delayed mode.