.. |spotmaxlogo| image:: _static/logo.png
   :width: 64
   :target: https://github.com/ElpadoCan/SpotMAX/tree/main/spotmax/resources

.. |githublogo| image:: images/github_logo.png
   :width: 32
   :target: https://github.com/ElpadoCan/SpotMAX

.. _GitHub: https://github.com/ElpadoCan/SpotMAX

.. _Francesco Padovani: https://www.linkedin.com/in/francesco-padovani/

|spotmaxlogo| Welcome to SpotMAX!
=================================

Multi-dimensional microscopy data analysis
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

*Written in Python 3 by* `Francesco Padovani`_

|githublogo| Source code on `GitHub`_

Here you will find all you need to master our tool! 

If you need to **analyse fluorescence microscopy data** you are probably in the 
right place.

SpotMAX will help you with these **two tasks**:

1. Detect and quantify **globular-like structures** (a.k.a. "spots")
2. Segment and quantify **fluorescently labelled structures** (e.g., mitochondria, nucelus, etc.)

.. card-carousel:: 1

   .. card::
      
      .. figure:: images/home_carousel/spotmax_GUI.png

         Graphical User Interface

         Interactively set the analysis parameters
   
   .. card::
      
      .. figure:: images/home_carousel/C_elegans_halo.png

         Synaptonemal Complex in *C. elegans*

         Accurately detect touching spots
   
   .. card::
      
      .. figure:: images/home_carousel/Anika_mito_yeast.png

         Detect spots and segment a reference channel

         Segment and quantify the mitochondrial network in 3D
   
   .. card::
      
      .. figure:: images/home_carousel/Jette_stem_cells_telomeres.png

         Telomeres length quantification in stem cells (DNA-FISH)

         Quantify telomeres length as a function of cell size 
   
   .. card::
      
      .. figure:: images/home_carousel/Dimitra_smFISH.png

         Count single-molecule of mRNAs in smFISH data

         Optimised for high spot density
   
   .. card::
      
      .. figure:: images/home_carousel/inspect_results_GUI.png

         Inspect the results

         Annotate detected spots and inspect features by hovering on the spot

SpotMAX excels in particularly challenging situations, such as 
**low signal-to-noise ratio** and **high spot density**.

It supports **2D, 3D, 4D, and 5D data**, i.e., z-stacks, timelapse, and multiple 
fluorescence channels (and combinations thereof).

.. raw:: html

   <figure>

   <video width="100%" controls autoplay loop muted playsinline>
      <source src="_static/timelapse_yeast_mito.mp4" type="video/mp4" />
      <img src="_static/screenshot_timelapse_yeast_mito.png"
         title="Your browser does not support the video tag"
         alt="Timelpase microscopy of <i>S. cerevisiae</i> with detection of mitochondrial DNA and segmetnation of mitochondrial network. Dataset by Dr. Padovani F., Helmholtz Munich, Germany"
      >
   </video>

   <figcaption>Timelpase microscopy of <i>S. cerevisiae</i> with detection of mitochondrial DNA and segmentation of mitochondrial network.</figcaption>

   </figure>

Contents
========

.. toctree::
   :maxdepth: 2

   install/index
   misc/get_started
   run/index
   how_it_works/index
   parameters/index
   features/index
   misc/output_files
   run/gui/inspect_results_tab
   misc/training_ai
   tutorials/index
   misc/publications
   misc/contributing
   api/api
   misc/cite
   misc/logos