climax-rfglab 2025.10.5

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

or

$ uvx --from climax-rfglab climax

A CLImax executable will be created, which allows the tool to be run without uv. If the directory that contains 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.

A note for developers

If you want to download the code and run from source, you will first need to compile the part of CLImax that uses Rust. The simplest way to do that is to install maturin and run the following command within the CLImax folder:

$ maturin develop --release

After that, you can run CLImax with:

$ python -m climax.climax

Using CLImax

After installing CLImax with one of the methods above, You can invoke it with:

$ climax <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/fixtures/gray_stack.tif) ... :

    $ climax tests/fixtures/gray_stack.tif
  

• ... including zarr images (e.g. tests/fixtures/4D_stack.zarr):

    $ climax tests/fixtures/4D_stack.zarr
  

• 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
  

• Notice that if you try to open a color image, the channels will be displayed as different dimensions. Thus, for instance, if you open the CLImax logo:

• You can indicate the zoom factor initially used to display the image. Keep in mind that larger zoom values will take longer to render. The default value is 1.0, but you can select any of the values in climax.zoom_factors (currently 0.03125, 0.0625, 0.125, 0.25, 0.5, 1., 2., 4., 8., 16., and 32.):

    $ climax cells_movie.tif -z 2.0
  

The CLImax dashboard provides tools to display and manipulate images:

name	function
rotate	rotate 90° clockwise
flip h.	flip horizontally
flip v.	flip vertically
invert	invert color map
update	continuous/discrete update
x-y, z-y, z-x	slicing plane
auto	automated contrast adjustment (min-mode, max-99th percentile)

The dashboard also shows the histogram of the image currently on display. The histogram is updated in real time as the user explores the image.

A command bar provides additional functionality that can be invoked with the mouse or with several quick-keys:

key	function
.	next slice
,	previous slice
+	zoom in, uses nearest-neighbour or bilinear interpolation
-	zoom out, uses nearest-neighbour or bilinear interpolation
k	toggle dark mode on/off, initially off
o	open a new image
t	open an image sequence (select a folder)
i	toggle bilinear interpolation on/off, initially off (i.e. nearest neighbour interpolation)

CLImax today

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

Citing CLImax

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

Sponsors

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