Removed references to accounts (#122)

Author: kjy5

source/pinpoint/development.md

@@ -65,7 +65,7 @@ Manager classes handle the high-level coordination of functionality in Pinpoint.
 
 #### Function code
 
-Function classes handle the isolated functionality of specific features in Pinpoint. For example, the code allowing control of the Camera is an isolated functionality. Other examples include the Accounts system, Ephys Link, the Rig code, etc.
+Function classes handle the isolated functionality of specific features in Pinpoint. For example, the code allowing control of the Camera is an isolated functionality. Other examples include Ephys Link, the Rig code, etc.
 
 #### Modules
 

source/pinpoint/tutorials/tutorial_basics.md

@@ -1,5 +1,11 @@
 # Trajectory Planning
 
+<div style="border: 1px solid #f5c2c7; background-color: #f8d7da; color: #842029; padding: 1em; border-radius: 0.5em; margin: 1em 0;">
+  <strong>⚠️ Important:</strong><br>
+  The accounts system is now <strong>deprecated</strong> and will be removed in the coming months.<br>
+  Please use <strong>Pinpoint v1.x</strong> to access your data in the meantime.
+</div>
+
 Press [ESC] at any time to open the help and settings menu.
 
 <div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden;">
@@ -63,7 +69,7 @@ The Probe panel provides easy access to the information about the active probe i
 
 The three buttons on the top right **lock** the probe (preventing accidental keyboard or mouse movements), **duplicate** the probe in the scene, and **download** the probe data to the clipboard. You can paste the copied data into any text editor.
 
-The bottom row has the **Accounts dropdown** where you can choose which experiments this probe is saved in, as well as the **snap to dura** button and **home** button.
+The bottom row has the **snap to dura** button and **home** button.
 
 The home button moves the probe back to the current reference coordinate (defined in the Atlas settings). The snap to dura button snaps the probe back to the surface of the brain, moving only along the depth axis. 
 
@@ -170,21 +176,6 @@ sub-menus.
 </div>
 <br>
 
-## Account
-
-The Accounts tab in the settings allows you to save insertions across computers.
-Insertions are stored in experiments. One insertion can be shared across
-multiple experiments.
-
-![Connect a probe to a manipulator](../../_static/images/tutorial/accounts.png)
-
-1. Register a new account, we kindly ask that you use an email address so that we can keep in touch about major updates to Pinpoint in the future. We won't give away your email or send a message more than once or twice a year.
-2. Log in to your account by providing the username and password. Leave the "stay logged in" toggle checked if you are on a private computer.
-3. Open the experiment edit panel to add and remove experiments and re-name them. Experiments are just buckets, you can use them in any way you want: to represent mice, to actually represent different experiments, to represent differents sets of insertions targeting particular brain regions, etc.
-4. Select the current active experiment from the dropdown. This will change the visible list of insertions below.
-5. The insertion list shows the insertions in the active experiment. You can rename insertions, delete them from the experiment, and enable/disable them in the 3D scene. Coming soon: we will add options to mark insertions as "recorded" so that we can calculate coverage maps for experiments.
-6. Any time your local data is out-of-sync with the data stored on the server the "unsaved changes" message will appear. If you are using Pinpoint in a browser **please note that unsaved changes do not get saved if you exit the browser**, the program auto-saves changes about once a minute. If you are using Pinpoint in a desktop app, exiting will automatically save all changes.
-
 ## Surgery
 
 To use your coordinates for a surgery, rotate the manipulator to match the azimuth angle (phi) and set the probe elevation angle (theta). Then move your probe tip to Bregma and zero your manipulator. (Optional: move your probe tip to Lambda and record the distance from Bregma to Lambda, then enter that into the Atlas settings in Pinpoint). We recommend using the technique shown in ![this reference](https://www.researchgate.net/figure/Schematic-diagram-of-stereotactic-surgery-and-variations-of-bregma-and-lambda-A-Dorsal_fig1_362675943) when estimating the position of Bremga and Lambda on the skull (i.e. align the "curve" between the sutures, not the exact point where they attach).

source/pinpoint/tutorials/tutorial_ephys_copilot.md

@@ -36,27 +36,9 @@
    while to open if it is updating. You may need to switch to it if other
    windows are in front.
 
-(create-load-experiment)=
-
-## 2. Create/load experiment
-
-You can use Pinpoint normally to plan an experiment. Alternatively, use the
-accounts system to load an experiment you've already created.
-
-1. Press <kbd>ESC</kbd> to open the main menu.
-2. Switch to the "Accounts" tab.
-   ![img.png](../../_static/images/tutorial/ephys_copilot/accounts_tab.png)
-3. Enter your username and password and press "Login". Your experiments and it's
-   probes will show up.
-   ![img.png](../../_static/images/tutorial/ephys_copilot/accounts_login.png)
-4. (Optional) Uncheck "Enable in scene" to hide the probes in the scene. Just
-   remember to re-enable them when you're ready to use them in step 9.
-   ![img.png](../../_static/images/tutorial/ephys_copilot/loaded_experiment.png)
-5. Press <kbd>ESC</kbd> to close the main menu.
-
 (create-dummy-probes)=
 
-## 3. Create dummy probes for visualization
+## 2. Create dummy probes for visualization
 
 1. Click the "Add new probe" button in the top right corner of the screen:
 
@@ -80,7 +62,7 @@ accounts system to load an experiment you've already created.
 
 (launch-ephys-link)=
 
-## 4. Launch Ephys Link
+## 3. Launch Ephys Link
 
 1. Press <kbd>ESC</kbd> to open the main menu.
 2. Switch to the "Ephys Link" tab.
@@ -96,7 +78,7 @@ accounts system to load an experiment you've already created.
 
 (configure-manipulators)=
 
-## 5. Configure manipulators
+## 4. Configure manipulators
 
 1. Set the handedness of each manipulator by selecting it from the dropdown.
    ![img.png](../../_static/images/tutorial/ephys_copilot/handedness_dropdown.png)
@@ -110,7 +92,7 @@ accounts system to load an experiment you've already created.
 
 (connect-dummy-probes)=
 
-## 6. Connect dummy probes to manipulators
+## 5. Connect dummy probes to manipulators
 
 1. Click the dropdown by "Link Probe" and select the probe you want to link to
    the manipulator.
@@ -127,7 +109,7 @@ calibrated to Bregma yet. We will do this in a later part.
 
 (activate-copilot)=
 
-## 7. Activate Copilot
+## 6. Activate Copilot
 
 1. Press the Enable Copilot Checkbox to activate the Copilot panel.
    ![img.png](../../_static/images/tutorial/ephys_copilot/enable_copilot.png)<br><br>
@@ -136,7 +118,7 @@ calibrated to Bregma yet. We will do this in a later part.
 
 (calibrate-manipulators-to-bregma)=
 
-## 8. Calibrate manipulators to Bregma
+## 7. Calibrate manipulators to Bregma
 
 1. **Get up and physically move** to your manipulators.
 2. **Manually** move a manipulator and touch the probe tip to Bregma.
@@ -157,13 +139,10 @@ vivo_ manipulators.
 
 (drive-manipulators-to-target)=
 
-## 9. Drive manipulators to target
+## 8. Drive manipulators to target
 
 1. Use the dropdown menu under each manipulator to select their target insertion
-   point. These options are from the experiment you created/loaded in part 2. If
-   you don't see any options, make sure you enable any probes you disabled from
-   the accounts tab and that the angles of the dummy probe match the angles of
-   the insertion.
+   point. If you don't see any options, check that your experiment probes have the same angles as your manipulators.
    ![img.png](../../_static/images/tutorial/ephys_copilot/select_target.png)
 2. With targets selected, lines will be drawn showing the path probes will take
    to reach their target entry coordinates.
@@ -182,7 +161,7 @@ target entry coordinates.
 
 (calibrate-to-dura)=
 
-## 10. Calibrate to the Dura
+## 9. Calibrate to the Dura
 
 1. **Get up and physically move** to your manipulators.
 2. **Manually** move a manipulator ventrally (on the **DV / Z** axis) until the
@@ -200,7 +179,7 @@ when the tip is back at the Dura.
 
 (punch-through-dura)=
 
-## 11. Punch through the Dura
+## 10. Punch through the Dura
 
 1. **Get up and physically move** to your manipulators.
 2. **Using the depth axis, manually** punch the probe tip through the Dura.
@@ -209,7 +188,7 @@ when the tip is back at the Dura.
 
 (drive-to-target-depth)=
 
-## 12. Drive to target depth
+## 11. Drive to target depth
 
 1. Set your desired drive speed with the slider and drive past distance. The
    defaults are 5 µm/s and 50 µm.
@@ -231,7 +210,7 @@ record data!
 
 (record-data)=
 
-## 13. Record data
+## 12. Record data
 
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