Managing your data
From the Biodock files screen, you can perform various operations on your files.

Copy and paste

You can duplicate files by either:
  • Right clicking a file or folder and selecting Make a copy
  • Selecting a file or folder and pressing Command+C (Control+C if you're on Windows), then navigating to where you want to paste your files, and pressing Command+P (Control+P).
    • When you copy the files, you should see a small popup that looks like this:

Cut and paste

You can also cut and paste files by pressing Command+X (Control+X if you're on Windows), then navigating to where you want to paste your files, and pressing Command+P (Control+P).
Note that cutting will remove the files from the original location and move them to the new location, while copying will preserve the files in the original location and increase your storage usage.

Move

You can move files in your file system by right clicking and selecting the Move option.
This will open a modal where you can select the new destination for the selected files.

View details

You can view additional details for a file or folder by either:
  • Right clicking on the file or folder and selecting View details
  • Clicking the i (info) button in the action bar.
This will open the file details sidebar which contains additional file information such as file size and dimensions, along with a higher resolution thumbnail of the image.

Download

You can download an image by right clicking a file or folder and selecting Download. This will download the file or a zip of the contents of the folder.

Merge

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.
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.