Running MY SOFTWARE
This page serves as a reference guide for MY SOFTWARE syntax - you must install before proceeding.
Refer to the tutorial for an example step-by-step guide for how to use MY SOFTWARE.
Description
MY SOFTWARE performs this task.
Input
An .ome.tiff and markers.csv file
Example markers file
The markers file should be formatted in this way
Output
A pyramidal, tiled .ome.tif
Usage:
MY SOFTWARE can be run with the following command
MY-SOFTWARE FILE [FILE ...] [OPTIONS]
For example, to run MY SOFTWARE on a set of data stored at my/path, with OPTION-Y set to 30:
MY-SOFTWARE FILE my/path --OPTION-Y 30
Required arguments
| Name | Description |
|---|---|
FILE |
an ome.tif image file to be processed |
Optional arguments
| Name; Shorthand | Description | Default |
|---|---|---|
--help; -h |
Show this help message and exit | |
--output DIR; -o DIR |
Write image files to DIR | Current directory |
--OPTION-Y |
Set the number to run with option y. Read below for more information about selecting a value for option y. | 5 |
OPTION Y
The default value works well in many cases, but increasing the value will do X. If you notice Y in your output, the value may need to be adjusted.