plate-tool/README.md

# plate-tool

A web-based tool for creating and visualizing picklists for your favorite (possibly acoustic) liquid handler.

## Table of Contents
- [Usage](#usage)
  - [Plates](#plates)
    - [Adding plates](#adding-plates)
    - [Modifying plates](#modifying-plates)
  - [Transfers](#transfers)
    - [Adding a transfer](#adding-a-transfer)
    - [Modifying transfers](#modifying-transfers)
  - [Importing and Exporting](#importing-and-Exporting)
    - [Export as CSV](#export-as-csv)
    - [Export as JSON](#export-as-json)
    - [Import from JSON](#import-from-json)
    - [Import Transfer from CSV](#import-transfer-from-csv)
  - [Other Neat Features](#other-neat-features)
- [Installation](#installation)

## Usage

### Plates
#### Adding plates
When you open plate tool for the first time,
you'll be greeted by a message informing you that no plates are selected.
     
To add a new plate, click the "Add" button for the corresponding plate type:
    
Once you've added at least one source plate and one destination plate,
click one of each to select them.
The right-most pane will now display these plates.

#### Modifying plates
Suppose you erroneously created a plate, or misspelled its name.
Double click on that plate in the list (top-left pane) and a new modal will open.
Here you can rename a plate or delete it.
You may also change the format of a plate
(note that this will not delete any data if you accidentally switch to a smaller format).

### Transfers
#### Adding a transfer
Now that you have two plates selected,
it's time to add a transfer.
We can see all of the properties of our transfer in the bottom-left pane.
You should first name your transfer (this name is only used for your reference, and is not passed to the liquid handler).
You can enter your source and destination regions in their respective fields;
the accepted format should be familiar—capital letters for the row and arabic numerals for the column.

However, it is much easier to click-and-drag the desired region.
If we click and hold on a well (see right pane), that specifies our start well.
Then, we can drag and subsequently release on our desired end well.

Our selected wells will be bolded (thicker outline).
You might also notice that some wells are hatched:
this indicates wells that will be used in the transfer.
Not all selected wells will necessarily be hatched,
depending on the transfer type and interleave settings.

When all of the settings are to your liking, click the "Save" button.
Note that it now appears in the "Transfers" section of the list pane.

#### Modifying transfers
If you already saved a transfer and would like to change it,
click on its entry in the list.
Now change the properties of the transfer as you did during initial creation.
When finished, click the "Save" button to commit these changes.

If you no longer need a transfer, select it as above and then click the "Delete" button.

#### Interleave
Interleave can be set for both source and destination plates.
Essentially, it can be read as "use every Nth well".
That is, a source row interleave of 2 would use every other row of the selected region.
It is permitted to have interleave in both dimensions on both plates in a single transfer.

#### Pooling
Consider a case where you want to condense an entire column in a source plate into just one row in the destination.
Instead of creating multiple transfers, it is sufficient to set the destination row interleave to 0.
An 0 interleave can be thought of as condensing that dimension to a point.
For this reason, 0 interleaves are not permitted on source plates (consider what this would represent).
Similarly, 0 interleaves are not permitted in replicate transfers (see next section).

#### Replicates
Where pooling permits a "many-to-one" transfer, replicates are "one-to-many".
This behavior is achieved by selecting a region in the destination plate instead of just a plate.
(If the corners of the destination region are not identical, it is a replicate.)

Plate-tool will attempt to fit as many copies into the selected destination region as space permits.
Partial copies will not be created.
That is, if a source region is 3 wells wide and a destination region is 7 wells wide,
2 copies will be made, and the 7th well in the destination will be left unused.

### Importing and Exporting

#### Export as CSV
Exporting the transfers we have created to a CSV format is the primary (if not sole) usage of Plate Tool.
To do so, first note the "File" tab at the top-left of the screen (above the list pane).
Mouse over this tab, and a few more options will be revealed.
We want to export: mouse over export and select "Export as CSV".
You will be prompted by your browser to select a location for your file.

As of version `0.4.0`, it is possible to pick a CSV export format:
Mouse over options, then export, then click "Change CSV export type".
In the dialog that opens, select your desired export type.
Currently, plate-tool supports:
  - Normal
    - This format can be imported by Cellario's cherrypick hook.
  - Echo Client
    - This format is useful if you want to run a picklist directly from the
    Echo Client software.
    This will export just the transfers between the currently selected plates;
    I assume you'd be using this feature in a non-automation context 
    and know to load your plates into your Echo yourself.

#### Export as JSON
##### (Saving Your Work)
Currently, it is not possible to export to a format produced by other similar software.
However, you might reasonably want to save a copy of your work
either as a backup or to share.
Mouse over the "File" tab, then "Export" as above, then alternatively select "Export as JSON". 
Your browser will then prompt you to pick a suitable location to save your work as a file.
(See note 1 below)

#### Import from JSON 
##### (Recovering Your Work)
If we want to import one such file, mouse over the "File" tab as before
and select "Import", and finally click "Import from JSON".
This opens a modal where you are prompted to upload (see note 2)
your file; it will then be processed and loaded.
Keep in mind that this will overwrite any work you currently have open,
so you may wish to export first (see above).

_Note 1_: JSON files are plaintext!
By default there is little whitespace (this makes comprehending them a challenge)
but if we pass it through a "JSON Beautifier" (enter this into your search engine of choice)
it immediately becomes more readable.
It is encouraged (although by no means necessary) to take a look at your export;
you will see that the representation here very closely mirrors the representation presented
in Plate Tool.

_Note 2_: Use of the word "upload" might imply that your data is leaving your computer.
It does not.
You are welcome to verify (use your browser's developer tools, it should have a network tab)
that this application does not "phone home".
Your data is stored locally (unless you choose to export it and distribute it yourself).

#### Import Transfer from CSV
##### (Using a picklist as a transfer)
If you have a CSV generated by another tool (or plate-tool),
you can import it as a single transfer.
To do so, mouse over the "File" tab, then "Import", and finally "Import Transfer from CSV".
When creating transfers via this method, the transfer cannot be edited.
This is useful if you have a pre-existing picklist that you would like to visualize in plate-tool.

You may either manually map plates in a picklist to plates you've already created, or click "Auto" to:
1. Generate all plates in the picklist
2. Generate transfers for all source:destination pairs.

_Note_: If you try to use this feature and no plates are available to select,
there was likely an issue parsing your picklist.
Your browser's console may have guidance as to why parsing failed;
plate-tool was probably expecting a different name for a column than was in your file.

_Note_: If you find a picklist that Cellario *can* import that plate-tool cannot,
please email me!
Odds are your picklist contains a weird edge case I've not considered,
and I would like to fix that!

### Other Neat Features

#### Taking Pictures of Plates
If you double click on a plate
(try to avoid clicking a well since that will change your selection)
plate-tool will do some magic to take a screenshot of your plate
and deposit it in your clipboard for you.
You can then paste this into PowerPoint, GIMP, or whereever else
you want a pretty picture of a plate.
I hope this is helpful for arts and crafts.

_NOTE:_ I won't guarantee this feature will work in all contexts;
it relies on your browser thinking that you have plate-tool open
in a "secure context" (localhost or https).

#### Turn off the in-transfer hashes
Have you noticed that when you select a transfer, the wells to
be used in that transfer have little diagonal lines over them?
Hopefully you have, because this is supposed to happen!
However, if you want to take a Pretty Plate Picture (see above),
you might want these indicators turned off.

To disable the indicators, mouse over "Options" (top-left of screen), then "Styles",
then click "Toggle transfer hashes".
To turn them back on, do the exact same thing.

#### Transfer Volume Heatmap (Experimental)
This can be used to verify that all of the wells in a plate will have the same volume
transferred at a glance.
Wells will be colored based on the sum of all transfers using that plate.

To toggle this feature, mouse over "Options", then "Styles", then click "Toggle volume heatmap".

_NOTE_: The scale for the colors is spaced linearly; if you have a well that is being used
significantly more than some others, it may be difficult to see the difference between other wells
with more similar volumes.
If you have a use case that would benefit from a logarithmic scale here, please let me know.

## Installation

Plate tool is hosted [here](https://ilia.moe/cool-stuff/plate-tool/) for your convenience.
However, you're absolutely welcome to host your own instance (even locally).
Here's how:
(_Note:_ If you run Windows you're absolutely fine to install rustup in Powershell, and the subsequent steps should be very similar but likely with different filepaths. I haven't personally validated this. )

1. Make sure you have a working Rust toolchain
    1. Installing `rustup` is the easiest way to do this. See [their website](https://rustup.rs/),
  or consult documentation provided by your distribution.
    2. Add the `wasm32-unknown-unknown` target with `rustup target add wasm32-unknown-unknown`
    - Generally, Rust's tools give descriptive errors and will help you solve problems yourself.
2. Install [trunk](https://trunkrs.dev/)
    - Run `cargo install --locked trunk`
3. Clone this repository using git
4. Enter the plate-tool-web directory and run `trunk serve`
     - You may need to check where `cargo` is installing binaries by default. For me, they're at `~/.cargo/bin`.
       If trunk is not automatically placed in your path, you would then run `/your/path/to/.cargo/bin/trunk serve`.
     - You can instead run `trunk build --release` for a more performant binary.

## Bug Reports and Further Help

Any requests for help or assistance with bugs can be sent to platetool(at)ilia.moe

If reporting a bug, ideally include what it was you were trying to do and, if possible, a screenshot or any logs in
your browser's console.