semvec/pypi-packages huggingface dataset:
synaptogram 0.0.11
Module for helping assess synapse counts
Requires Python: >=3.7

Synaptogram
===========

Introduction
------------

This facilitates screening synaptic ribbons identified in Imaris to determine
if they are artifacts or orphans (i.e., without a post-synaptic bouton). This
program will work with any Imaris file that contains the `Spots` feature named
`CtBP2`.

Using the program
-----------------

Three visualizations are provided:

* Overview image (upper left). When a ribbon is selected, the overview image
  updates to show the location of the synaptic ribbon (marked with a white
  circle) in the confocal image. This context can be useful for determining the
  status of a ribbon.
* Projection of the selected ribbon (lower left). Each channel (GluR2, CtBP2,
  and Myosin VIIa) are shown separately as maximum projections onto the XY, YZ
  and XZ planes. The crosshair shows the center of the ribbon in each image.
  Sometimes other ribbons will appear in the same image, so focus on the
  crosshair.
* Tiled overview of all ribbons identified by Imaris. The currently selected
  ribbon is indicated by a white square. Artifacts are indicated by red squares
  and orphans by green squares.

Ribbons in the tiled image are sorted by default based on the maximum intensity
of the GluR2 label. If needed, you can sort by other criteria. The goal is to
identify all ribbons that are artifacts (e.g., in the nucleus or outside the
cytoplasm of the inner hair cell) or orphans (i.e., no post-synaptic receptor
associated with the ribbon).

Mouse interaction
.................
left click + drag (overview and tiled ribbons)
    Pan image
right click (tiled ribbons visualization only)
    Select select ribbon for analysis.
mouse wheel (overview and tiled ribbons)
    Zoom in/out

Keyboard shortcuts
..................
These keyboard shortcuts only work when the tiled visualization has focus
(e.g., by left-clicking on it). The focus is set to the tiled visualization by
default, but can be lost if you click on one of the other visualizations in the
window.

a or d
    Mark ribbon as artifact
o
    Mark ribbon as orphan
c
    Clear label
arrow keys
    Navigate through the selected ribbons with the arrow keys. Scrolling off
    the end of one row will take you to the next row.
Ctrl + S
    Save the analysis
urtext 0.1.8
Urtext /ˈʊrtekst/ is a markup language and framework for programmable notebooks in text files on top of the Python language.

# Urtext Core Library

## This repository

This repository is the core Urtext library in Python. It has no user interface and requires an implementation in a text editor (see [Implementations](https://github.com/nbeversl/urtext?tab=readme-ov-file#sublime-text)).

## What Urtext Is

Urtext /ˈʊrtekst/ is an open-source syntax and interpreter for plaintext writing, research, documentation, knowledge bases, journaling, Zettelkasten, project/personal organization, note taking, a lightweight database substitute, or any other writing or information management that can be done in text format. See https://urtext.co for more information.

## Implementations

Currently there are implementations for Desktop (Windows/Mac/Linux) using [Sublime Text](https://www.sublimetext.com/) and iOS using [Pythonista](https://omz-software.com/pythonista/).

### Sublime Text 

The implementation in Sublime Text is a [Sublime Text Package](https://www.sublimetext.com/docs/packages.html), with all dependencies, that also includes a syntax definition, themes, and default keybindings. Its repository is [https://github.com/nbeversl/UrtextSublime](https://github.com/nbeversl/UrtextSublime).

It can be installed using Package Control, **though it has its own package control channel**.

Installation instructions are here: [https://urtext.co/setup/sublime-text/](https://urtext.co/setup/sublime-text/).

### iOS

There is an implementation for iOS using [Pythonista](https://omz-software.com/pythonista/). The repository for this implementation is at [urtext_pythonista](https://github.com/nbeversl/urtext_pythonista) and utilizes [Sublemon](https://github.com/nbeversl/sublemon), a simple custom editor created just for this implementation that provides syntax highlighting and a custom keyboard.

An [install script](https://github.com/nbeversl/urtext_pythonista_install_or_update) is available that downloads all dependencies in a single step. For instructions, see that repository or [https://urtext.co/setup/ios-using-pythonista/](https://urtext.co/setup/ios-using-pythonista/).

## Questions and Issues

All questions and support requests may be submitted to the webform https://urtext.co/support/ (no login needed).

Developer questions and issues with this core library may be submitted to [the issues tab](https://github.com/nbeversl/urtext/issues). For issues with specifical implementations, please submit to the issues tabs of the those repositories.