Merging channels

Biodock exposes a feature for merging single channel image files into 3D multichannel images. If you have single channel images for which you want to run Nuclear Cell Segmentation analysis, you will have to merge your single channel images into multichannel images.

In the filesystem make a selection of image files that need to be merged into 1 or more multichannel images. Click the ellipsis options menu in the top right or right click optionally. The merge option should appear.

Merging through example

In this example, we are going to merge 5 images into a set of two multichannel images. One set is 2 files with the prefix of Hepatocytec and another set is 3 files with a prefix of test.

In the modal that appears, the regex input determines the naming conventions of your resulting 3D merged files and which channels get applied to which file. The regex requires two capture groups - one to identify the groupings of files that get merged together and a second group specifying the changing channels within each group.

In this example, a regex of '(Hepatocytec|test)(1|2|3)' splits the files into 2 groups.

The first capture group of Hepatocytec|test splits the 2 files with the prefix of 'Hepatocytec' into one group and the the 3 files with the prefix of test into another. The result will be two 3D files of Hepatocyec and test.

The second capture group of 1|2|3 specifies the changing channels between files within each group. The result is the merge of test1, test2, test3 into one single file test with channel 1 applied to test1, channel 2 to test2 and channel 3 to test3. In the Hepatocytec group - we apply channel 1 to Hepatocytec1 and channel 2 to Hepatocytec3.

By default, the channel regex group applies the channel ordering in alphanumeric ascending order, i.e - channel 1 gets applied to Hepatocytec1 and test1, channel 2 to Hepatocytec3 and test2., etc...

You can reverse the order of the channel application by checking the box to reverse order in channel settings -

A notification will appear that your merge is in progress. Once Biodock's system completes the merge, a folder will be created in your filesystem in the same location where you made your selection of files. This folder will contain your merged 3D multichannel image files, which in our example are Heptocytec.tif and test.tif.

Below is the viewer of the merged 3D file test.tif. The image has 3 channels, comprising of the 3 files captured over 3 different channels which have been merged as specified by the settings we had input earlier on this page.

Channel appears first in file name

The merge regex by default sets the second capture group to identify channel values. With advanced settings, you can flip the capture group ordering so files that have channel appearing first can be matched with the first regex group.

Regex can become complex but it is flexible enough to support the naming conventions and desired grouping conventions of your image files. See Examples for help on specifying the merge settings to merge your single channel images.


1) Files -

  • ControlMAP2X1.tif

  • ControlNOMAP1X3.tif

  • ControlSOMETHINGELSEX6.tif

  • ControlOTHERx8.tif

The regex to merge these files into a single file Control.tif -

(Control).+(x[1-9]) - matches the prefix common to all files first -- Control. Then matches any character any number of times -- until the 2nd group match of 'x followed by a number between 1 & 9.

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