climax-rfglab 2025.4.13

climax is a Command Line IMAge eXplorer

CLImax (a Command Line IMAge eXplorer)

Installing CLImax

We recommend that you install CLImax as a tool using uv:

$ uv tool install climax-rfglab

Doing this will result in the placement of the CLImax executable in a bin directory in the PATH, which allows the tool to be run without uv. If the directory with the CLImax executable is not in the PATH, a warning will be displayed and the following command can be issued to add it to the PATH:

$ uv tool update-shell

CLImax can also be installed as a regular Python package using uv:

$ uv pip install climax-rfglab

or pip:

$ python3 -m pip install climax-rfglab

A note on the Python interpreter

CLImax requires that you have Python 3.10 or above installed.

Using CLImax

How you run CLImax depends on how you chose to install it.

If you installed CLImax as a tool using uv, then you can invoke CLImax with:

$ climax <filename>

If you installed CLImax as a Python package, you can run it as:

$ python3 -m climax.py <filename>

You can also run CLImax without installing it, taking advantage of uvx:

$ uvx --from climax-rfglab climax <filename>

There are a few ways to open an image with CLImax:

• You can specifiy the path to the image that you want to open (e.g. tests/cells_movie.tif) :

    $ climax tests/cells_movie.tif
  

• Or you can indicate a folder (slices in this example) that contains an image sequence:

    $ climax ./slices
  

• If there are image channels split into different files, you can specify a group of substrings to distinguish which files in the folder belong to which channel. For example, to open the files in the slices folder containing the substrings '488' and '561' as two different channels:

    $ climax ./slices -s 488 561
  

• You can use a list of paths to concatenate sideways (i.e. display side-by-side, but all the images must have the same dimensions!!):

    $ climax cells_movie_1.tif cells_movie_2.tif
  

• You can specify the color map used to display the image. The color map defaults to 'gray'. Check here for a list of color maps.

    $ climax cells_movie.tif -c viridis
  

JuNkIE provides access to the standard matplotlib toolbar, and also includes a second toolbar with additional functionality:

icon	function
	rotate 90° clockwise
	flip horizontally
	flip vertically
	invert color map
	hide/show axes
	continuous/discrete update

JuNkIE today

As we develop and improve JuNkIE, there may be small changes to the user interface. This is how JuNkIE looks as of today:

Citing JuNkIE

If you use JuNkIE, please cite this repository. We are working on the paper!

Adding functionality onto JuNkIE

If you would like to extend JuNkIE, please check out JuNkIE-picasso, a JuNkIE fork that allows you to define arbitrary image processing pipelines and integrate them into JuNkIE.

Sponsors

We are grateful for the generous support from the following agencies and institutions, which contribute to the development and maintenance of JuNkIE: