the big photo move

developer-guide/03-Background jobs/03-avoiding-od.md

@@ -78,6 +78,6 @@ enable_dodging_od=1
 
 The diagram of timing, actions, and OD reading, looks like the following:
 
-![](/img/developer-guide/background_job_dodging_timing.png)
+![](/img/developer-guide/03-background-jobs/03-avoiding-od/background_job_dodging_timing.png)
 
 And you're done!

developer-guide/07-Plugins/02-adding-plugins-to-ui.md

@@ -17,7 +17,7 @@ You should have already added your plugin's Python code to your Pioreactor by so
 
 ### Adding a custom background job to the list of activities
 
-![](/img/developer-guide/activities.png)
+![](/img/developer-guide/07-plugins/02-adding-plugins-to-ui/activities.png)
 
 
 The list of activities, among other things, is sourced from either of two directories:
@@ -52,11 +52,11 @@ published_settings:
 
 Saving it to either directory above, and refreshing the page:
 
-![](/img/developer-guide/activities_with_example.png)
+![](/img/developer-guide/07-plugins/02-adding-plugins-to-ui/activities_with_example.png)
 
-![](/img/developer-guide/settings_with_example.png)
+![](/img/developer-guide/07-plugins/02-adding-plugins-to-ui/settings_with_example.png)
 
-![](/img/developer-guide/card_with_example.png)
+![](/img/developer-guide/07-plugins/02-adding-plugins-to-ui/card_with_example.png)
 
 
 ### Adding a custom Python script to the list of activities
@@ -84,7 +84,7 @@ See more information on the structure of your script [here](/developer-guide/int
 
 Suppose we wish to add our new automation, either installed from a package or via the `plugins` folder, to the drop-down list of automations users can choose from:
 
-![](/img/developer-guide/dropdown_automations.png)
+![](/img/developer-guide/07-plugins/02-adding-plugins-to-ui/dropdown_automations.png)
 
 This list is sourced from yaml files located on the leader's Raspberry Pi, in either of two directories:
  - `/var/www/pioreactorui/contrib/automations/`, is the source of the our built-in automations
@@ -119,9 +119,9 @@ fields:
 
 If this file was saved to the folder `/home/pioreactor/.pioreactor/plugins/ui/contrib/automations/dosing`, we would see the following in the web interface (after refreshing):
 
-![](/img/developer-guide/dropdown_automations_with_example.png)
+![](/img/developer-guide/07-plugins/02-adding-plugins-to-ui/dropdown_automations_with_example.png)
 
-![](/img/developer-guide/automations_example.png)
+![](/img/developer-guide/07-plugins/02-adding-plugins-to-ui/automations_example.png)
 
 More examples of automation [yaml files here](https://github.com/Pioreactor/pioreactorui/tree/master/contrib/automations).
 

developer-guide/07-Plugins/03-plugin-as-python-package.md

@@ -151,7 +151,7 @@ function decorated with `@run.command` at the bottom of the file. See example [h
 
 This configuration file will contain additional configs that we want to add to our list of existing Configurations on the Pioreactor web interface. This file will be merged with the existing `config.ini` when the plugin is installed. 
 
-![](/img/developer-guide/python-package-new-config.png)
+![](/img/developer-guide/07-plugins/03-plugin-as-python-package/python-package-new-config.png)
 
 :::tip
 A convention we've tried to follow is to use the section name convention of `[<job_name>.config]` or `[<automation_name>.config]` in the configuration files. For example, our relay job has `[relay.config]` in its `additional_config.ini` and settings under it.
@@ -399,13 +399,13 @@ There are two ways to do this:
 1.	Create an issue to have us edit the plugins.json file for you. 
 2.	Fork from our repository to edit the plugins.json file, then create a pull request. 
 
-![](/img/developer-guide/python-package-pull-or-issue.png)
+![](/img/developer-guide/07-plugins/03-plugin-as-python-package/python-package-pull-or-issue.png)
 
 In both cases, we will evaluate your plugin to ensure code quality and all requirements are met.
 
 Once your plugin is accepted, it will appear on the Plugins tab on the Pioreactor web interface. Users in the community can now easily click _Install_ to download your plugin onto their Pioreactors!
 
-![](/img/developer-guide/python-package-plugins.png)
+![](/img/developer-guide/07-plugins/03-plugin-as-python-package/python-package-plugins.png)
 
 
 ### Troubleshooting

developer-guide/10-Hardware/05-pinout.md

@@ -5,4 +5,4 @@ hide_table_of_contents: true
 ---
 
 
-![](/img/developer-guide/pinout.png)
+![](/img/developer-guide/10-hardware/05-pinout/pinout.png)

developer-guide/20-User interface/04-adding-charts.md

@@ -6,7 +6,7 @@ hide_table_of_contents: true
 
 You can add custom charts to the UI. Below is an example of adding a chart that displays historical and real-time CO2 sensor data.
 
-![custom chart of CO2 reading](/img/developer-guide/custom_chart.png)
+![custom chart of CO2 reading](/img/developer-guide/20-user-interface/04-adding-charts/custom_chart.png)
 
 ### Step 1
 Create a yaml file with the following fields, and place it in `/home/pioreactor/.pioreactor/plugins/ui/contrib/charts/`. (Plugins can put the yaml file under `ui/contrib/charts` in there project folder - it will be added upon installation.)
@@ -41,7 +41,7 @@ co2_readings=1
 ...
 ```
 
-![](/img/developer-guide/adding_chart_to_config.png)
+![](/img/developer-guide/20-user-interface/04-adding-charts/adding_chart_to_config.png)
 
 ### Troubleshooting
 

developer-guide/99-architecture.md

@@ -4,4 +4,4 @@ slug: /architecture
 hide_table_of_contents: true
 ---
 
-![The Pioreactor system architecture](/img/developer-guide/arch.png)
+![The Pioreactor system architecture](/img/developer-guide/99-architecture/arch.png)

experiments/02-Secondary level education/01-control-testing.md

@@ -17,7 +17,7 @@ Conduct a simple control test to evaluate results between Pioreactors, using the
 
 ## Requirements
 
-<AssemblyInstructionBlock images={["experiments/three_pioreactors.jpg"]}>
+<AssemblyInstructionBlock images={["experiments/02-secondary-level-education/01-control-testing/three_pioreactors.jpg"]}>
 
 *   At least two available Pioreactors
 *   Dry baker's yeast
@@ -41,7 +41,7 @@ With all factors the same, you should see similar normalized OD and growth rate
 
 Here are graphs we generated though our A/A test: 
 
-![](/img/experiments/aa-test-results.png)
+![](/img/experiments/02-secondary-level-education/01-control-testing/aa-test-results.png)
 
 These kinds of tests make it easy to identify any unusual activity occurring in a specific Pioreactor (i.e, if it is missing an LED, temperature malfunctions, etc). In our case, though, both ran almost identically! Thus, we conclude that reliable comparisons can be drawn between these Pioreactors. 
 
@@ -56,4 +56,4 @@ These kinds of tests make it easy to identify any unusual activity occurring in
 6. Select _Manage all Pioreactors_, and start _Stirring_ activity, _Temperature automation_ activity (set to an optimal temperature; ex. 30°C) and _OD reading_ activity.
 7. Confirm that everything looks normal (ex: receiving optical density signal).
 8.	Back on the _Pioreactors_ page, select _Manage all Pioreactors_ and start _Growth rate_. It will take a minute for results to begin showing up. 
-9. Watch growth progress on the _Overview_ page.
+9. Watch growth progress on the _Overview_ page.

experiments/02-Secondary level education/caffeine-inhibition.md

@@ -17,7 +17,7 @@ Use caffeine-containing liquids to inhibit the growth of your culture.
 
 ## Requirements
 
-<AssemblyInstructionBlock images={["experiments/three_pioreactors.jpg"]}>
+<AssemblyInstructionBlock images={["experiments/02-secondary-level-education/01-control-testing/three_pioreactors.jpg"]}>
 
 *   At least two available Pioreactors
 *   Dry baker's yeast
@@ -40,7 +40,7 @@ We used two Pioreactors and two vials containing 15 mL of YPD media. We added 1
 
 The growth rate chart clearly demonstrates an inhibition of growth occurring in the sample containing tea:  
 
-![](/img/experiments/tea2-exp-results.png)
+![](/img/experiments/02-secondary-level-education/caffeine-inhibition/tea2-exp-results.png)
 
 ## Recommendations 
 
@@ -60,4 +60,3 @@ We recommend trying different amounts of tea, coffee, or other caffeine containi
 8. Confirm that everything looks normal (ex: receiving optical density signal).
 9.	Back on the _Pioreactors_ page, select _Manage all Pioreactors_ and start _Growth rate_. It will take a minute for results to begin showing up. 
 10. Watch growth progress on the _Overview_ page.
-

experiments/02-Secondary level education/low-vs-high-conc-media.md

@@ -17,7 +17,7 @@ Conduct a simple comparison of yeast growth between a low percent and high perce
 
 ## Requirements
 
-<AssemblyInstructionBlock images={['experiments/media_exp.jpg']}>
+<AssemblyInstructionBlock images={['experiments/02-secondary-level-education/low-vs-high-conc-media/media_exp.jpg']}>
 
 *   At least two available Pioreactors
 *   Dry baker's yeast
@@ -58,7 +58,7 @@ We inoculated both with 100 uL of a yeast slurry using a micropipette. If this i
 
 As expected, growth diminished earlier for the culture inoculated in 1% YPD: 
 
-![](/img/experiments/ypd-conc-exp.png)
+![](/img/experiments/02-secondary-level-education/low-vs-high-conc-media/ypd-conc-exp.png)
 
 
 ## Recommendations 
@@ -80,4 +80,3 @@ Consider lower or higher bounds for your media compositions. How much sooner wil
 9.	Back on the _Pioreactors_ page, select _Manage all Pioreactors_ and start _Growth rate_. It will take a minute for results to begin showing up. 
 10. Optional: you can change the names of the Pioreactor in the UI to display the percent of media. 
 11. Students can watch growth progress on the _Overview_ page.
-

experiments/02-Secondary level education/salt-stress-on-yeast.md

@@ -20,7 +20,7 @@ Use your Pioreactor to model how cells are affected by high salt (hypertonic) so
 
 ## Requirements
 
-<AssemblyInstructionBlock images={["experiments/salt_materials.jpg"]}>
+<AssemblyInstructionBlock images={["experiments/02-secondary-level-education/salt-stress-on-yeast/salt_materials.jpg"]}>
 
 *	At least two available Pioreactors
 *	Dry baker's yeast
@@ -61,7 +61,7 @@ To each vial, 0g, 0.225g, 0.45g, 0.675g and 0.9g of table salt were added, respe
 
 After approximately 26 hours, the following growth rates were recorded: 
 
-![](/img/experiments/salt_growth_rate.png)
+![](/img/experiments/02-secondary-level-education/salt-stress-on-yeast/salt_growth_rate.png)
 
 We can summarize our results in the following table to highlight our data: 
 
@@ -104,4 +104,3 @@ The flexibility of the Pioreactor means you can do much more with this simple co
 11.  Confirm that everything looks normal on the _Overview_ page (ex: receiving optical density signal).
 12.	Back on the _Pioreactors_ page, select _Manage all Pioreactors_ and start _Growth rate_. 
 13.  Watch the growth progress on the _Overview_ page! 
-

experiments/02-Secondary level education/yeast-growth-by-temperature.md

@@ -20,7 +20,7 @@ Demonstrate the effect of temperature on yeast growth.
 
 ## Requirements
 
-<AssemblyInstructionBlock images={["experiments/two_pio_plus_vials.jpg"]}>
+<AssemblyInstructionBlock images={["experiments/02-secondary-level-education/yeast-growth-by-temperature/two_pio_plus_vials.jpg"]}>
 
 *   At least two available Pioreactors
 *   Dry baker's yeast
@@ -44,9 +44,9 @@ The following experiment was performed using four Pioreactors. Four vials contai
 
 Over the course of 12 hours, the following graphs were recorded: 
 
-![](/img/experiments/temperature_temp.png)
+![](/img/experiments/02-secondary-level-education/yeast-growth-by-temperature/temperature_temp.png)
 
-![](/img/experiments/temperature_growth_rate.png)
+![](/img/experiments/02-secondary-level-education/yeast-growth-by-temperature/temperature_growth_rate.png)
 
 Though subtle, non-linear patterns of growth rate are observed between the temperatures. Key data points are summarized in the following table: 
 

experiments/02-Secondary level education/yeast-in-ethanol.md

@@ -113,7 +113,7 @@ This technique produces halving ethanol percentages of 0%, 1.5%, 3%, and 6% to b
 
 After approximately 18 hours, the following implied growth rates were recorded:
 
-![](/img/experiments/ethanol_gr.png)
+![](/img/experiments/02-secondary-level-education/yeast-in-ethanol/ethanol_gr.png)
 
 We can summarize our results in the following table: 
 

experiments/03-University level education/01-algae-day-night-cycle.md

@@ -16,7 +16,7 @@ This experiment will show the growth curve of algae over a 20h:4h day/night cycl
 
 ## Requirements
 
-<AssemblyInstructionBlock images={["experiments/algae_exp.jpg"]}>
+<AssemblyInstructionBlock images={["experiments/03-university-level-education/01-algae-day-night-cycle/algae_exp.jpg"]}>
 
 * At least one available Pioreactor
 * Algae
@@ -41,7 +41,7 @@ Typical experiments use a 16h:8h day night cycle, but we've adjusted the time pe
 
 For this style of experiment, let's investigate our normalized OD results: 
 
-![](/img/experiments/nod_algae_intensity.png)
+![](/img/experiments/03-university-level-education/01-algae-day-night-cycle/nod_algae_intensity.png)
 
 Adjusting just one factor (light intensity) where one is twice as high as the other yielded an approximate doubling of growth in the vial subjected to higher light intensity! 
 
@@ -76,4 +76,3 @@ Change the names of the Pioreactor in the UI to organize your vials.
 12.	Watch the growth progress on the Overview page.
 
 
-

experiments/04-Research and beyond/temp-cycle.md

@@ -42,7 +42,7 @@ Check out our [blog post](https://pioreactor.com/blogs/pioreactor/using-custom-a
 
 Once we [exported our data](/user-guide/export-data), we charted our yeast growth rate against the temperature readings to generate the following graph:
 
-![](/img/experiments/yeast_growth_vs_temp.png)
+![](/img/experiments/04-research-and-beyond/temp-cycle/yeast_growth_vs_temp.png)
 
 ## Recommendations 
 

user-guide/01-getting-started/00-gettingstarted.mdx

@@ -34,13 +34,12 @@ import Card from '@site/src/components/Card';
     <Card imageUrl="user-guide/hardware-assembly/upgrade-version-splash.png" headerText="Pioreactor 20ml v1.0 → v1.1 upgrade kit" linkUrl="/user-guide/v11-upgrade-hardware-setup"/>
     <Card imageUrl="user-guide/add-teh/14_teh_finished.jpeg" headerText="Temperature Expansion Kit" linkUrl="/user-guide/temperature-expansion-kit" />
     <Card imageUrl="user-guide/hardware-assembly/pioreactor_dosing_splash.webp" headerText="Adding peristaltic pumps" linkUrl="/user-guide/using-pumps" />
-    <Card imageUrl="user-guide/leds_splash.webp" headerText="Adding more LEDs" linkUrl="/user-guide/using-leds" />
+    <Card imageUrl="user-guide/01-getting-started/00-gettingstarted/leds_splash.webp" headerText="Adding more LEDs" linkUrl="/user-guide/using-leds" />
 </div>
 
 <h3> Software guides</h3>
 
 <div className="cardGrid">
-    <Card imageUrl="user-guide/choose-next.png" headerText="Software installation" linkUrl="/user-guide/software-set-up" />
+    <Card imageUrl="user-guide/01-getting-started/00-gettingstarted/choose-next.png" headerText="Software installation" linkUrl="/user-guide/software-set-up" />
 </div>
 
-