GUI usage

Prerequisites

Before starting any analysis please ensure that the following conditions are fulfilled

• You have enough space on your data partition

• ClearMap2.1 is installed and up to date

• Fiji (as in Fiji is Just ImageJ) is installed and up to date. (if you want to open your file in .tif)

• You have a folder containing the sub-folders with your raw data.

Start ClearMap

There are 2 ways to start the software:

• Use the start menu entry

• Use the terminal:

  • Open the terminal (CTRL+ALT+T) and type

    conda activate ClearMapUi
    clearmap-ui
    

    Note

    Note that other commands starting with clearmap (e.g. utilities) will also become available after installing

Software introduction

The software contains the following tabs which correspond to different operations:

Sample • Alignment • CellMap • Vasculature • Batch

The preferences of the software are controlled through 2 ways:

• The Edit -> preferences menu for the general preferences

• The config files starting with _default in the

  $HOME/.clearmap folder for the analysis defaults

Hint

For each control, you can hover the control label to get a hint as to its function. More help is available for some controls through a icon on the right of the control, whenever some detailed explanation is deemed necessary.

When setting integer values, if max is required (e.g. max image intensity), use –1 as per the python notation.

Note

In the Data Viewer, if you cannot see your sample, then

1. ensure that the LUT is set correctly on the right.

2. right-click on the middle of the image and select View all.