Welcome to brainmap9000's TL;DR page!

brainmap9000's window is composed of several portions. The main one is the map portion:

Within the map portion, you can scroll your mousewheel to view currently unseen parts.
Also, if you hold Ctrl + scroll your mousewheel the map will zoom in and out (according to the scroll's direction).

On top of the map portion, you can find the text displayer portion, which displays text based on the object in the map you are currently hovering your mouse on:

On the left side of the window you can find the buttons portion, which contains clickable buttons (for more details see sections 2, 3 and 4):

Near the top left corner you will see the menubar portion, which contains pop-up menus ('File', 'View') which allow you to perform some actions (see sections 5, 6, 7, 8, 9 and 10):

Hover your mouse over a region. You will now see the name of that region appear in a text displayer, located in the window's upper part.

Try clicking one of the buttons located in the windows left side. Clicking a button will cause it's pathway to appear on the map in the form of arrows.

Hovering over an arrow will display the arrow\"neuron"'s pre-synaptic region, it's post-synaptic region, it's pathway's name, and it's "stage" within the pathway.

Try clicking the 'Areas' tab located within the window's left portion.

Clicking a button from this tab (which contains areas) will cause all the "inputs" and "outputs" of the given region to appear on the map (i.e. all of its pre-synaptic and post-synaptic neurons).

Let's say you are interested to see only sensory pathways. Go to the 'tags' tab. Click the 'Sensory' tag.

If you will now return to the 'Tracts' tab you will see only the tracts which have been tagged with the 'Sensory' tag. If you check the 'Areas' you should see only areas which are part of pathways which have been tagged with the 'Sensory' tag.

Adding pathways:

- Open the 'File' menu in the window's menu bar (located near the upper left corner).
- Click the "Add a Tract\Pathway" option

- You will now see this window:

- Enter your pathway's name in the name field
- Try typing your pathway's first stop in the 'beginning' field. You will see suggestions pop up. Important note: you can only fill the stop input fields with a valid region name (i.e. a region that appears on the map and has been synced with the program (for more information about syncing see 10).
- Add the pathway's remaining stops.
If you want to add a region to a stop, press the little plus button at the bottom of that stop.
If you want to add more stops, press the bigger plus button at the right.
You can delete a region in a stop by right-clicking it then pressing "Delete".
- Choose neurotransmitters if you want
- When you're done, click the 'Add Tract' button

Editing pathways:

- Open the 'File' menu.
- Click the "Edit a Tract\Pathway" option

- You will now see this window:

- Type in the pathway you wish to edit, then click the 'load' button
- You will now see the pathway appear in editable form, similar to how it would appear if you were to add it:

- Edit your pathway. Same rules apply here as in the pathway adding explanation.
- Click the "Save Tract" button.

Note: you can also edit a pathway by right-clicking the pathway's button, then pressing the "Edit Tract" option.

Removing pathways:

- Open the 'File' menu.
- Click the "Remove a Tract" option

- You will now see this window:

- Type in the pathway you wish to delete, then click "Remove Tract"

- To add a new tag to the program (which you can then use to tag pathways with), first open the 'File' menu.
- Click the "Add\Remove a Tag" option

- You will see this window:

- Click the 'Add a Tag' option
- Enter your tag's name in the "tag name" field:

- Click the 'add' button
- Note: you can also remove tags in a similar way by clicking the 'Remove a Tag' option.

To view the simplified figures of currently active (pressed) pathways, first open the 'View' menu, then click the "Simplified Figure View" option.

You can also access a pathway's simplified figure by right-clicking the pathway's button, then choosing "Show Simplified Figure View".

To view the descriptions of currently active (pressed) pathways, first open the 'View' menu, then click the "Description View" option.

You can also access a pathway's description by right-clicking the pathway's button, then choosing "Show Description".

- Open the 'File' menu, then click the 'Add\Edit Neurotransmitter' option.

- You can add a new neurotransmitter by pressing the 'add a neurotransmitter' button.
- You can change a neurotransmitter's color by clicking its color square or by right-clicking it, then pressing 'change color'.
- You can delete a neurotransmitter by right-clicking its color square, then pressing remove.

Disclaimer: You cannot do this by solely using 'brainmap9000'.

In order to add a new area to the map, you'll first need to draw this area in the map using some vector graphics painting software. I recommend you to use Inkscape. It's completely free and simple to use. You can download it using this link:https://inkscape.org/release/

After downloading Inkscape, open the 'map1.svg' file in Inkscape. This file is located in brainmap.9000's directory. You should see something like this:

Click the pencil tool (tools are located on the right side):

Choose a stroke and fill. Hold SHIFT+click a color to choose a stroke. Click on color regularly to choose a fill. There are some colors to choose from on the bottom.

Hold the mouse to draw your area...
Important TIP: if you want to draw more complex shapes (such as a cortex for example), use the pencil/pen to draw only the outline (black stroke, transparent fill), then use the paint bucket tool.

After finishing, you should see your area appear within the "Layers and Objects" portion on the right. It should have a name like "path(somenumber)"-

Rename your area to your desired name (by double-clicking on it in the "Layers and Objects" portion)

Save the file (hold Ctrl+S).
That should be it! Close Inkscape and now open brainmap9000.
You should see your area appear on the map:

BUT, you won't be able to include your area in a pathway yet. In order to enable that, open the 'File' menu, then click 'Sync Map':

You should now see a small window with a button that says "Check For New Areas". Click the button. The window should now display a list of areas. One of those areas is the area you've added.

Click your area in order to sync it with the map. Once you click, a tree like menu should appear. Navigate it to find your area's desired parent area (this allows for the area to be included in group area buttons such as 'Thalamus' for example. If you don't care about this you can just click NODES).

When you find it, choose it with your mouse, then click the 'pick' button (bottom right corner).

Congratulations! You've synced your area with the map. If you will now try to add a new pathway (by opening the "Add a Tract\Pathway" option in the 'File' menu) and try to type in your area in the area fields you will now see it appear as a valid option: