Experiment
In Tango an experiment corresponds to a set of acquisitions that are to be analyzed in the same way.
Project
Projects are sets of experiments. You can choose a created project or create a new one; You can also delete a project, all associated data will be lost.
New Project
Creates a new Project.
Delete Project
Deletes the selected project, and all contained experiments.
Experiment
An experiment corresponds to a set of acquisitions that are to be analyzed. You can choose an already created experiment or create a new one; You can also delete an experiment, all associated data will be lost. You can also rename an experiment.
New Experiment
Creates a new Experiment. No special characters. Names must be unique.
Delete Experiment
Deletes the selected experiment, all data associated will be lost.
Rename Experiment
Renames the selected experiment. No special characters. Names must be unique.
Duplicate
This command allows one to create a new experiment with all the settings of the current experiment. Data (images and measurements are not duplicated)
Type a new name and choose a destination project, then click NewXP.
Override
This command allows one to override settings of the selected experiment on other experiments.
Calibration
If use global scale is unchecked, calibration contained in metadata of each image will be used for each image.
Otherwise, the calibration has to be defined, and will be used for all data.
Import File Method
Choose Bioformat-LOCI if your data are:
- in a format compatible with bioformats.
- in a single file containing all you channels.
If your images are in the .tif format (one .tif file corresponding to one channel): the associated images can be stored in two different ways :
- Keyword: All images are saved in the same directory, and channels are identified by a special keyword (like C=0).
- Only the keyword must differ between files of the same acquisition. Names are upper/lower case sensitive.
- all the images of a given acquisition must be in the same directory.
In the Field tab, when adding Fields, select the directory containing the tiff files (all subdirectories will also be scanned for tiff files).
- File order : All files corresponding to a given field are stored in a single directory. Files will be opened according to their numbering in the folder (in the case of two channels file1 = channel1, file2=channel2, file3=channel1, ...).
In the Field tab, when adding Fields, select the parent directory containing the subdirectories corresponding to your fields.
Import Images
Browse to select the directory or files you want to open according to the import method chosen above.
If you select one file or multiple files, only the selected files will be opened. If you select a directory, all files inside the folder will be opened, data inside sub-folders will also be opened.
The loaded images will be displayed in the Data panel.
Save
Save your changes.
Edit Experiment Structure
Channel Images
An acquisition consists in one or more channels files, in Tango the first channel corresponds to the nucleus (or any containing structure). Click Add to add channels and then
click Edit to edit the channels parameters. Indicate the keyword use to identify the channels (it can be a text like C=0 or a numbering order 0,1. In case there is a shift between channels
indicate the X, Y and Z shift values (in pixels). You can also remove some channels.
Structures
In Tango structures corresponds to the different nuclear compartments of interest.
Structures are dissociated from channels.
However usually there is one structure per channel.
In more complex cases you may want to analyze two different compartments in a same channel (like DAPI that can both defines the nuclei and chromocenters). A structure is associated to a processing chain.
Click Add to create a new structure, and Edit to set-up its parameters. Indicate the name of the structure (the name of your biological structure like gene-MLL or your protein). The first structure is always the nucleus (or any containing structure). Indicate the acquisition channel associated with the structure. The Settings correspond to the algorithm that will be used to segment this structure (see Processing Chain). Finally indicate the Color that will be used to display the structure.
Virtual Structures
This section will be documented later.
Quantitative Image Analysis
You can add and edit the different quantitative measurements you want to perform on your structures. Choose the measurements in the list of plugins (see the developer pages on how to create plugins for Tango). Edit the settings for the measurements. Edit also the names (keys) of the measurements and if you want to perform them or not. All measurements are automatically applied to all objects in a structure. See Quantification module page.
Measurement on individual objects
Basic measurements on objects include volume measurement, elongation by a fitting ellipsoid, ... See MeasureGeometrical.
Signal Quantification plugin
This plugin allows basic 3D intensity measurements on detected objects in a specified channel, like average, deviation, minimum and maximum intensity. It can also compute the Integrated density, that is to say the sum of intensity inside a object. See Measure Statistics.
Distances
This plugin will compute all object to object distances between two structures. All distances are in units. See Distances.
Three distances are available :
- Center to center distances, between the centers of the two objects.
- Center to border distances, the minimum distance from the center of the first object to the other.
- Border to border distances, the minimum distance between two objects (equals 0 in case of co-localization).