fused and more links

CamDavidsonPilon · CamDavidsonPilon · commit a0546c08aeec · 2026-02-04T21:31:59.000-05:00
diff --git a/static/img/user-guide/30-advanced/25-od-fused-biomass/od-angle-sensitivity.jpg b/static/img/user-guide/30-advanced/25-od-fused-biomass/od-angle-sensitivity.jpg
diff --git a/user-guide/02-Experiment basics/05-Activities.md b/user-guide/02-Experiment basics/05-Activities.md
@@ -4,16 +4,16 @@ slug: /activities
 hide_table_of_contents: true
 ---
 
-Below is a list of activities that come available with the Pioreactor. Additionally, you can add activities using plugins. [Read more about using plugins](/user-guide/using-community-plugins).
+Below is a list of built-in activities that come with the Pioreactor. Additionally, you can add activities using plugins. [Read more about using plugins](/user-guide/using-community-plugins).
 
-- **Stirring**: this starts the stirring in the Pioreactor. After starting to stir, you can change the stirring speed in the Settings tab. You can modify the default stirring speed in the configuration settings. We recommend keeping the stirring range of 150 RPM to 600 RPM.
+- **Stirring**: starts the stirring in the Pioreactor. After starting, you can change the stirring speed in the **Settings** tab. You can modify the default stirring speed in the configuration settings. We recommend keeping the stirring range between 150 RPM and 600 RPM.
 
-- **Optical density**: this turns on the system that measures culture density. Readings will start to populate the _Experiment Overview_ page. It's useful to inspect the first few minutes of readings to ensure the readings are as expected (e.g., the readings aren't erratic, and the stirring speed is appropriate, etc.).
+- **Optical density**: turns on the system that measures culture density. Readings will start to populate the **Experiment Overview** page. It's useful to inspect the first few minutes to ensure the readings look reasonable (for example, they aren't erratic and the stirring speed is appropriate). Read more about [optical density and normalization](/user-guide/od-normal-growth-rate).
 
-- **Growth Rate**: this activity requires that stirring and optical density be running as well. This starts the calculation of a normalized optical density, and the implied growth rate. Both calculations will populate the _Experiment Overview_ page.
+- **Growth Rate**: this activity requires that stirring and optical density be running as well. It starts the calculation of a normalized optical density and the implied growth rate. Both calculations will populate the **Experiment Overview** page. Read more about [growth-rate modelling](/user-guide/growth-rate-modelling).
 
 - **Temperature automation**: turning on a temperature automation will start collecting temperature readings. For example, the **Thermostat** automation will use a feedback loop to stabilize the Pioreactor to a set temperature. Pausing an automation will cease both any active heating and temperature data collection. Stopping an automation will stop the heating and temperature collection. To change a running temperature automation, use the "Change Temperature Automation" button. Read more about specific [temperature automations](/user-guide/temperature-automations).
 
-- **Dosing automation**: turning on a dosing automation to start listening periodically for dosing triggers. A dosing automation requires at least 1 pump to be available and calibrated. [More about using pumps](/user-guide/using-pumps). Pausing a dosing automation will stop any currently, and future, dosing occurring until the automation is unpaused. Read more about the different types of [dosing automations](/user-guide/dosing-automations).
+- **Dosing automation**: turning on a dosing automation starts listening periodically for dosing triggers. A dosing automation requires at least 1 pump to be available and calibrated. [More about using pumps](/user-guide/using-pumps). Pausing a dosing automation will stop any current and future dosing until the automation is unpaused. Read more about the different types of [dosing automations](/user-guide/dosing-automations).
 
-- **LED automation**: turning on a LED automation to start listening periodically for LED change triggers. Read more about [LED automations](/user-guide/led-automations).
+- **LED automation**: turning on an LED automation starts listening periodically for LED change triggers. Read more about [LED automations](/user-guide/led-automations).
diff --git a/user-guide/02-Experiment basics/09-od-normal-growth-rate.md b/user-guide/02-Experiment basics/09-od-normal-growth-rate.md
@@ -9,9 +9,9 @@ import AssemblyInstructionBlock from '@site/src/components/AssemblyInstructionBl
 import Highlight from '@site/src/components/Highlight';
 import Admonition from '@theme/Admonition';
 
-### Background on optical density 
+### Background on optical density
 
-The interaction of light within samples of suspended microorganisms will differ from light passing through concentrated solutions. Instead of being absorbed, light is scattered by the cells in suspension. This scattered light is measured as **optical density (OD)**. As turbidity increases, more scattering occurs, resulting in a higher OD reading. 
+Light passing through a culture behaves differently than light passing through a clear solution. Instead of being absorbed, light is scattered by the cells in suspension. This scattered light is measured as **optical density (OD)**. As turbidity increases, more scattering occurs, resulting in a higher OD reading.
 
 ![](/img/user-guide/02-experiment-basics/09-od-normal-growth-rate/absorption_vs_od.png)
 
@@ -21,9 +21,9 @@ Looking to calibrate for OD600 readings? [Visit this page](/user-guide/calibrate
 
 ### Normalization
 
-Due to manufacturing variables such as differences in LED strength and sensitivity, the raw OD readings can't be compared against each other. Instead, we use the _normalization_ technique described below:
+Due to manufacturing variation (LED strength and sensor sensitivity), raw OD readings can't be compared directly across devices. Instead, we use the _normalization_ technique described below:
 
-A series of initial OD readings are averaged to produce a _reference value_ (denominator). New OD readings after the reference value are normalized using the following simple equation: 
+A series of initial OD readings are averaged to produce a _reference value_ (baseline). New OD readings after the reference value are normalized using the following simple equation:
 
 $$
 \frac{\normalsize \text{latest\thickspace OD}}{\normalsize \text{reference\thickspace OD}}=\text{normalized\thickspace OD}
@@ -43,25 +43,25 @@ It's difficult to compare raw OD readings since the starting values are differen
 
 $\frac{\small 0.033}{\small 0.030}=1.1$
 
-Culture growth by 1.1x. 
+Culture has grown by 1.1x.
 
 ###### Pioreactor2
 
 $\frac{\small 0.015}{\small 0.010}=1.5$
 
-Culture growth by 1.5x. 
+Culture has grown by 1.5x.
 
 We can more accurately compare culture growth using these ratios as opposed to using the raw OD values. 
 
 :::tip
-Because of the way we defined _normalized_ optical density, it has the following easy interpretation: its the multiplicative amount the culture has changed by. So if the normalized OD is 2.0, the culture has doubled its initial concentration, i.e. doubled the population since the volume is fixed. This also works for traditional OD600 measurements: if your initial sample has OD600 equal to 0.45, then a normalized OD of 2.0 is the same as an OD600 of twice that, or 0.90. (Generally...).
+Because of the way we defined _normalized_ optical density, it has the following easy interpretation: it's the multiplicative amount the culture has changed by. So if the normalized OD is 2.0, the culture has doubled its initial concentration, i.e. doubled the population since the volume is fixed. This interpretation also maps to traditional OD600 measurements: if your initial sample has OD600 equal to 0.45, then a normalized OD of 2.0 is approximately an OD600 of twice that, or 0.90.
 :::
 
 ### Blanking
 
 While basic normalization accounts for initial OD differences, it does not consider the optical density of the media itself. For a more accurate growth rate calculation, you can blank your sample.
 
-Blanking your vials is recommended for experiments that begin with low OD readings (ex. inoculating small amounts of yeast). By blanking, you are able to observe the OD of only the microorganism of interest. 
+Blanking your vials is recommended for experiments that begin with low OD readings (e.g., inoculating small amounts of yeast). By blanking, you observe the OD of only the microorganism of interest.
 
 As an example, let's consider the same data as above, but this time we have information on the blank ODs: 
 
@@ -70,7 +70,7 @@ As an example, let's consider the same data as above, but this time we have info
 | Pioreactor1     |  0.025   | 0.030         		          | 0.005                        | 0.033     |
 | Pioreactor2     |  0.005   | 0.010	    			      | 0.005                        | 0.015     |
 
-We can now subtract the _blank_ values from the _latest OD_ and _reference OD_ values:
+We can now subtract the _blank_ values from both the _latest OD_ and _reference OD_ values:
 
 $$
 \frac{\normalsize \text{latest\thickspace OD}-\text{blank\thickspace OD}}{\normalsize \text{reference\thickspace OD}-\text{blank\thickspace OD}}=\text{blanked\thickspace normalized\thickspace OD}
@@ -80,24 +80,24 @@ $$
 
 $\frac{\small 0.033-0.025}{\small 0.030-0.025}=1.6x$
 
-Culture growth by 1.6x. 
+Culture has grown by 1.6x.
 
 ###### Pioreactor2
 
 $\frac{\small 0.015-0.005}{\small 0.010-0.005}=2x$
 
-Culture growth by 2x.
+Culture has grown by 2x.
 
 By accounting for the OD of the blank media, we are able to calculate a more accurate growth rate. 
 
 ### Growth rate
 
-We inoculated two vials with a drop of re-hydrated yeast, and tracked their growth at temperatures 27°C and 35°C. The following normalized optical density chart was generated by the Pioreactor:
+We inoculated two vials with a drop of re-hydrated yeast, and tracked their growth at temperatures 27°C and 35°C. The UI shows the following normalized optical density chart:
 
 ![](/img/user-guide/02-experiment-basics/09-od-normal-growth-rate/temp_normal_od.png)
 
 
-From the normalized optical density, an implied growth rate graph is generated. The relationship between the implied growth rate, $\text{gr}$ and the normalized optical density, $\text{nOD}$ is exponential, defined by the following equation:
+From normalized optical density, the UI also computes an implied growth rate. The relationship between the implied growth rate, $\text{gr}$, and the normalized optical density, $\text{nOD}$, is exponential and can be written as:
 
 $$
 \text{nOD}(t) =  \exp{ \left( \int_0^t \text{gr}(s)ds \right)}
@@ -109,16 +109,16 @@ $$
 \text{gr}(t)= \frac{ \text{nOD}'(t)} {\text{nOD}(t)}
 $$
 
-which plainly states that the growth rate is the rate of change of the size of the culture, normalized by the size of the culture.
+This states that the growth rate is the rate of change of the culture size, normalized by the culture size.
 
 
-This rate can give insight on the state of your culture under different external conditions.
+This rate helps compare the state of your culture under different conditions (temperature, media, etc.).
 
 ![](/img/user-guide/02-experiment-basics/09-od-normal-growth-rate/temp_growth_rate.png)
 
-These graphs can be interpreted in 4 phases:
-* The lag phase: No observed growth, but high cell activity. In this stage, cells are in a nutrient rich environment and are preparing for growth by synthesizing proteins and other necessary molecules. 
-* Exponential (or log) phase: Cells are now dividing and doubling in numbers after each generation time. Generation times are dependent on the species you are using for your experiment. 
+These graphs can be interpreted in four phases:
+* The lag phase: Little observed growth, but high cell activity. Cells acclimate to a nutrient-rich environment and prepare for division. 
+* Exponential (or log) phase: Cells divide and double at a roughly constant rate. Generation times depend on species and conditions. 
 * Stationary phase: Eventually the growth of cells reaches a plateau as nutrients are used up and waste products accumulate. At this point, the number of dividing cells will equal the number of dying cells.
 * Decline (or death) phase: As nutrients are depleted, cell growth slows while cell death increases.
 
@@ -128,7 +128,7 @@ Here's how these phases would apply to our graphs, focusing on the 35°C vial:
 
 ![](/img/user-guide/02-experiment-basics/09-od-normal-growth-rate/nod_interpretation.png)
 
-Some things to note: 
+Some things to note:
 * The lag phase can be detected easily in the growth rate graph, as the rate is stable and doesn't begin increasing until a bit after 6 PM. This is not easily determined in the nOD graph, since at this point the overall turbidity of the culture is low.
 * The exponential phase occurs when the growth rate is high/increasing. 
 * When the culture reaches the stationary phase, growth rate drops to 0 since the culture is no longer growing in size. The turbidity is constant.
@@ -142,10 +142,10 @@ When working with **small amounts** of a microorganism, or when using very turbi
 <AssemblyInstructionBlock title="How to record a blank" images={["user-guide/02-experiment-basics/04-set-up-an-experiment/calibrate.png","user-guide/02-experiment-basics/04-set-up-an-experiment/blank.png"]}>
 
 1. Insert your sterile vial containing media into the Pioreactor before inoculating with your species of interest.
-2. On the website, click the _Pioreactors_ tab on the left-hand menu, and choose one of the active Pioreactors.
-3. Select _Calibrate_, and under the _Blanks_ tab, click _Start_. The Pioreactor will now record the optical density of the blank vial.
+2. In the UI, click the **Pioreactors** tab on the left-hand menu, and choose one of the active pioreactors.
+3. Select **Calibrate**, and under the **Blanks** tab, click _Start_. The Pioreactor will now record the optical density of the blank vial.
 4. Repeat for all the Pioreactors to be used.
     *   A notification will appear when a Pioreactor has finished blanking.
-6. You can now inoculate your vials and begin your experiment.
+5. You can now inoculate your vials and begin your experiment.
 
 </AssemblyInstructionBlock>
diff --git a/user-guide/02-Experiment basics/10-manual-led-dosing.md b/user-guide/02-Experiment basics/10-manual-led-dosing.md
@@ -8,19 +8,19 @@ hide_table_of_contents: true
 
 ### Dosing
 
-You can run the pumps from the Pioreactor UI. These are NOT automations, but rather simple actions to use to set up an experiment, perform cleaning, or intervene in an experiment.
+You can run the pumps from the Pioreactor UI. These are not automations, but simple actions used to set up an experiment, perform cleaning, or intervene mid-run. For automated workflows, see [dosing automations](/user-guide/dosing-automations).
 
 #### Cycling
 
-Under the _Dosing_ tab, you run the media pump or the alt-media pump _and concurrently the waste pump_. This is called _cycling_. By running the waste pump simultaneously, the vial will avoid overflow. You can cycle for a set duration of time.
+Under the **Dosing** tab, you run the media pump or the alt-media pump _and concurrently the waste pump_. This is called _cycling_. Running the waste pump simultaneously helps avoid overflow. You can cycle for a set duration of time.
 
 ![UI showing how to cycle media.](/img/user-guide/02-experiment-basics/10-manual-led-dosing/cycle_media.png)
 
 Cycling is good for cleaning pumps, priming tubes with media, or filling your vial with media.
 
 #### Specific control of pumps
 
-Under the _Dosing_ tab, you can also run specific pumps (media, waste, and alt-media) for a specific duration, volumes (if calibrated), or continuously. The latter will run until the *Stop* button is pressed.
+Under the **Dosing** tab, you can also run specific pumps (media, waste, and alt-media) for a set duration, volume (if calibrated), or continuously. The latter will run until the *Stop* button is pressed. Read more about [using pumps](/user-guide/using-pumps).
 
 :::caution
 Careful not to overflow your vial! The Pioreactor doesn't know how much liquid is currently in the vial. Stay well below the max volume of the vial for safety.
@@ -30,13 +30,13 @@ Careful not to overflow your vial! The Pioreactor doesn't know how much liquid i
 
 #### Adjustments from manual changes
 
-Sometimes you may want to add or remove liquid from the vial manually. These changes can be recorded by using the _Manual adjustments_ form under the _Dosing_ tab. These do not run the pumps, but will log the adjustments. This is useful for recording adjustments into the database, and keeping metrics accurate.
+Sometimes you may want to add or remove liquid from the vial manually. These changes can be recorded by using the **Manual adjustments** form under the **Dosing** tab. This does not run the pumps, but logs the adjustments. This keeps metrics accurate.
 
 ----
 
 
 ### LEDs
 
-Under the _LED_ tab, you can update specific intensities of the LEDs.
+Under the **LED** tab, you can update specific intensities of the LEDs. For automated light schedules, see [LED automations](/user-guide/led-automations).
 
-![UI showing how to change LEDs.](/img/user-guide/02-experiment-basics/10-manual-led-dosing/change_leds.png)
+![UI showing how to change LEDs.](/img/user-guide/02-experiment-basics/10-manual-led-dosing/change_leds.png)
diff --git a/user-guide/03-Extending your Pioreactor/04-Experiment Profiles/10-experiment-profiles-schema.md b/user-guide/03-Extending your Pioreactor/04-Experiment Profiles/10-experiment-profiles-schema.md
@@ -1,7 +1,6 @@
 ---
 title: Experiment profile schema and syntax
 slug: /experiment-profiles-schema
-hide_table_of_contents: true
 ---
 
 Experiment profiles are YAML files that choreograph jobs across your Pioreactor cluster. This page documents the syntax the UI validates against and the constructs available when you are editing a profile directly.
diff --git a/user-guide/30-Advanced/20-estimators.md b/user-guide/30-Advanced/20-estimators.md
@@ -4,6 +4,7 @@ slug: /estimators
 sidebar_label: Estimators
 description: Learn how Pioreactor estimators turn raw sensor signals into derived measurements.
 sidebar_class_name: sidebar-item--updated
+hide_table_of_contents: true
 ---
 
 Estimators turn raw sensor signals into derived measurements that are more useful for experiments. They are similar to calibrations in lifecycle (created through a protocol, saved to disk, optionally set active), but they solve a different problem: they combine or transform measurements from multiple sensors into a single estimate.
diff --git a/user-guide/30-Advanced/25-od-fused-biomass.md b/user-guide/30-Advanced/25-od-fused-biomass.md
