Sources & Reference

Sources & Reference > Source Image > All Channels

Inserts a single node with an overlay of all channels present in the current image.

Sources & Reference > Source Image > Channels

Inserts a parental node with channels present in the source image. The channels can be selected in the drop-down menu.

Sources & Reference > Source Image > Combined Channels

Produces picture outputs representing both, the All channel composition and the individual channels.

Sources & Reference > Source Image > Selected Channels

Inserts a parental node with one channel selectable from the list of available channels (Selected) and the second channel with all the remaining channels together (Other).

Sources & Reference > Source Image > MxN pixels

Creates a new color image (channel) using the specified dimensions (Width, Height) and bit depth and fills it with the specified value.

Sources & Reference > Source Image > Deep Sim

Inserts a Deep SIM image.

Sources & Reference > Source Image > Deep Sim z-stack

Inserts a Deep SIM Z-Stack image.

Sources & Reference > Source Binary > Binaries

Inserts all binary layers found in the source image and selected in the drop-down menu.

Sources & Reference > Source Binary > Selected Binaries

Inserts a parental node with one output containing the binary layer selectable from the list of available binary layers (Selected) and a second output with all the remaining binaries together (Other).

Sources & Reference > Source Binary > Single Binary

Inserts a binary node using a segmentation selected in the drop-down menu.

Sources & Reference > Source Binary > ROI

Inserts a ROI node using ROI(s) from the current image.

Sources & Reference > Source Table > Load Results

Inserts a table node showing the selected Result from the chosen Analysis and Module.

Sources & Reference > Merge Tables > Load & Concatenate

Loads the result table specified by the Result Name from database and appends the content of the connected table to it. When the result table does not exist, the connected table is set as the result. It is useful when some analysis (statistics, classification) has to be calculated over all runs, not just the current one. In such a case use the result R to perform the analysis on.

Result Name

Name of the result table from database.

Result Matching

Sets the synchronizing rule for appending connected table's content (truncate when different columns / synchronize columns).

Add Extra Column

Adds extra columns for distinguishing analysis runs by Filename or Run Index.

Sources & Reference > Merge Tables > Concatenate HDF5

Not documented yet.

Sources & Reference > Parameters > Input Folder

Defines the folder used as an input. Click ... and select the folder.

Sources & Reference > Parameters > Input Number

Defines the input value.

Sources & Reference > Parameters > Input Text

Defines the input text.

Sources & Reference > Import > Color Image

Imports a color image from the specified path.

Sources & Reference > Import > Binary from ND2

Imports a binary/Global ROI from the specified nd2 file.

Sources & Reference > Import > Binary from CSV

Loads a binary layer consisting of rectangular objects representing bounding rectangles or centers of original binary objects. The main purpose of this node is the visualization of objects predicted by AI nodes. Optionally the objects' probability can be taken into account and objects can be filtered according to it.

The source table is assumed to be accumulated for the whole dimension and the first column represents the dimension index. The following columns are mandatory and represent the bounding rectangles' positions in pixels:

  • xmin - left edge

  • xmax - right edge

  • ymin - top edge

  • ymax - bottom edge

    The label column is also mandatory and stands for binary layers name. The prob column filled with objects probabilities is optional.

    Source table example:

    Table 12. 

    tindexxminyminxmaxymaxlabelprob
    010253601033373sperm0.9998
    0366478372491sperm0.9998
    111863511198358sperm0.9997
    1250926318sperm0.9997
    26626577272sperm0.9995

    Filename

    Source table location.

    Loop

    The table dimension representation.

    Label

    The desired label searched in source table data.

    Minimum probability

    Filter for prob column (when present).

    Rectangle/Center

    Selects one of the binary layer types being loaded (bounding rectangles or centers of original binary objects).

Sources & Reference > Import > Table from CSV

Imports a table from a comma separated values file (.csv). A data type (number or text) is determined for every column. The header (if present) can force the column type and a specific column meaning. Following header syntax is recognized:

Name or Keyword [Unit] : Type

Name

Any name except colon.

Keyword

For special columns like _Entity, _ObjId or _ObjId3d.

Unit

Any unit. This is an optional item.

Type

Is int for integer; number, real, double for real numbers and string, text for strings. This is an optional item.

Table 13. Example

_ObjIdSize [m] : numberDescription : text
11258reference object


Filename

Source table location.

Header

Indicates that the first row is a header (not actual data).

Separator

Is used to delimit columns (comma , (default), tabulator TAB or semicolon ;).

Sources & Reference > Import > Table from HDF5

Loads a table from HDF5 file.

Table can be:

  • an ordinary 2D dataset (row x columns) containing atomic datatypes or variable length strings,

  • a table previously exported using Table to HDF5 (group of column datasets).

When the format is not recognized table is not loaded.

Filename

Path to the file containing the table.

Location in file

Group or dataset in the file e.g. /Ga3Tables/Records.

Sources & Reference > Export > Color to Single TIFs

Exports TIFF images to the specified folder with the given name. This action can be used for having a reference when GA3 is used more than once JOBS.

Folder

Path where the TIFF images will be saved.

Name

Name of the TIFF files.

Numbering

If numbering is set to None, a single file is created. This file is overwritten with every frame of the new data. This is useful for single frame or reduced files from the ND Processing nodes. The two other options create one TIFF file per frame:

  • Append sequential number: C:\seq00000.tiff

  • Append loop fields C:\seq00000z000.tiff

Sources & Reference > Export > Binary to SVGs

Exports objects from the connected binary layer into .svg images.

Folder

Destination folder for saving the created file.

Name

Created file name.

Numbering

If numbering is set to None, a single file is created. This file is overwritten with every frame of the new data. The two other options create one .svg file per frame:

  • Append sequential number: C:\seq00000.svg

  • Append loop fields C:\seq00000z000.svg

Fill Opacity

Sets fill opacity of the exported object.

Stroke Opacity

Sets stroke opacity of the exported object.

Sources & Reference > Export > Split to Multipoint

Creates new nd2 file from cropped regions of the original one represented as a multipoint loop. Frames are ordered according to the selected column from the input table. Other loops (Timelapse, ZStack) are preserved.

Folder

Destination folder for saving the created file.

Name

Created file name.

Name Suffix

Suffix of the created files in case of saving to separate files (other loops than Timelapse and ZStack exist).

Multipoint Index Column

Column from the input table determining the cropped regions order in the resulting multipoint loop.

Center X Column

Column from the input table determining the center X of the cropped region in pixels.

Center Y Column

Column from the input table determining the center Y of the cropped region in pixels.

Width

Width of the cropped region.

Height

Height of the cropped region.

Note

Preview creates a filename with a Preview prefix.

Sources & Reference > Export > Table to CSV

Exports the table into a .csv (Comma Separated Values) file.

Filename

Name of the file and the path where it will be saved.

Truncate the file before each run

Deletes the file content with each GA3 run.

Delete

Deletes the file content.

Sources & Reference > Export > Table to HDF5

Stores a table into a HDF5 file.

Filename

Path to the file containing the table.

Location in file

Group or dataset in the file e.g. /Ga3Tables/Records.

Delete the table before each run

Sets whether the table is cleared before it is written to or appended.

Note

Preview creates a filename with Preview prefix.

Sources & Reference > Temporary > Load Last Color

Loads data previously saved with the Save Last node. The data is shared in the specified loop and kept private in other loops.

Store Name

Name of the storage used to distinguish the temporary stores.

Loop

Loop where the data is shared (<none> to share in all loops).

Set Invalid As

Specifies the substitution when the storage is invalid (zero/max intensity/current image).

Sources & Reference > Temporary > Save Last Color

Saves the data to temporary storage. The data is shared in the specified loop and kept private in other loops.

Note

The B input must be connected to the Load node to ensure that it is executed before the Save.

Store Name

Name of the storage used to distinguish the temporary stores.

Loop

Loop where the data is shared (<none> to share in all loops).

Sources & Reference > Temporary > Load Last Binary

Loads data previously saved with the Save Last node. The data is shared in the specified loop and kept private in other loops.

Store Name

Name of the storage used to distinguish the temporary stores.

Loop

Loop where the data is shared (<none> to share in all loops).

Set Invalid As

Specifies the substitution when the storage is invalid (empty/full/current binary).

Sources & Reference > Temporary > Save Last Binary

Saves the data to temporary storage. The data is shared in the specified loop and kept private in other loops.

Note

The B input must be connected to the Load node to ensure that it is executed before the Save.

Store Name

Name of the storage used to distinguish the temporary stores.

Loop

Loop where the data is shared (<none> to share in all loops).

Sources & Reference > Temporary > Load Last Table

Loads data previously saved with Save Last node. The data is shared in the specified loop and kept private in other loops.

Store Name

Name of the storage used to distinguish the temporary stores.

Loop

Loop where the data is shared (<none> to share in all loops).

Set Invalid As

Specifies the substitution when the storage is invalid (empty/current table).

Sources & Reference > Temporary > Save Last Table

Saves the data to temporary storage. The data is shared in the specified loop and kept private in other loops.

Note

The B input must be connected to the Load to ensure that it is executed before the Save.

Store Name

Name of the storage used to distinguish the temporary stores.

Loop

Loop where the data is shared (<none> to share in all loops).

Sources & Reference > Wizard > Visible Channels

Defines which channels (the connected ones) are shown in the wizard, whether autoscale LUTs is turned on and whether a pseudocolor is used for their visualization.

Sources & Reference > Wizard > Visible Binaries

Defines which binary layers (the connected ones) are shown in the wizard, whether the object IDs are shown and how the binary layer transparency is set.

Sources & Reference > Wizard > Visible Tables

Defines which tables (the connected ones) are shown in the wizard.

Sources & Reference > Save to Document > Save Pictures

Saves all connected channels into the result document. Connected inputs are synchronized by the ToBeStored property of the channel outputs present in the analysis.

Sources & Reference > Save to Document > Save Binaries

Saves all connected binaries into the result document. Connected inputs are synchronized by the ToBeStored property of the binary outputs present in the analysis.

Sources & Reference > Save to Document > Save Tables

Saves all connected tables into the result document. Connected inputs are synchronized by the ToBeStored property of the table outputs present in the analysis.

Sources have to be added explicitly and the source node needs a GUI for channel mapping or binary selection.