Opens all files supported by Bio-Formats. Depending on how the files are layout internally the interactive preview functionality of BDP2 may be slower than using below [ Open File Series ...] command, which have been optimised for reading data into BDP2. Please share your experiences with us!
Big image data, due to its size, is often distributed across several files. BigDataProcessor2 provides several ways to open such file series. Most flexible is the "Open File Series..." command, where regular expressions (see below) are used to specify how the different files compose a 5D (x,y,z,c,t) image data set.
Currently we support specific flavours of Tiff and HDF5 file series.
For Tiff we support single (x,y) plane Tiff and multi-plane Tiff files. In multi-plane Tiff files all planes must have the same size as they are loaded as one 3D volume with the Tiff planes corresponding to the z-position. Different channels and time points must be distributed across different files.
For HDF5 we support file series where each file contains a single 3D dataset, which must be a 3D array with dimension order z,y,x. This array will be loaded as one 3D volume. Different channels and time points must be distributed across different files.
For convenience, we also provide few commands to open commonly occurring file series, such that users do not have to enter the regular expressions:
Opens one folder with tiff files, each containing only a single plane, using the regular expression "(?<Z>.*)", which means that the whole filename is used to indicate the z-position of the plane in this file (using the natural sorting of files).
Opens one folder with tiff files, each containing only a single plane, using the regular expression ".*--t(?<T>\d+)--Z(?<Z>\d+)--C(?<C>\d+).*", to open files with names such as "Position001_Target--t00--Z00--C00.tif".
Opens a series of HDF5 files, each HDF5 file containing one 3D volume. The channels and timepoints are encoded in the file and/or sub-folder names, yielding regular expressions such as: ".*stack_6_(?<C1>channel_.*)/(?<C2>Cam_.*)_(?<T>\d+).h5".
Regular expressions are a powerful way to subset and group files.
Regular expression documentation
"(?<Z>)", "(?<C>)" and "(?<T>)" denote the z-slice, channel and timepoint groups, respectively.
".*" matches anything
"\d+" matches a sequence of numbers, e.g. 001
Below examples are on purpose without file extensions. The file extensions can be selected via a drop down in the "Open..." menu item and will be added to the regular expression automatically.
Below examples work both with and without zero-padding, e.g. "T0000", "T0001" works, but also "T0", "T2", "T11" works (and will have the correct numeric-based ordering). Also, the numberings do not have to start with 0 but can also start with a higher number, e.g., 1.
| (?<T>.*) | One file contains a one volume, there is only one channel, but several time points. This works for filenames such as "image-0000" and "image-0001". |
| (?<Z>.*) | One file contains a one z-plane, there is only one channel and one timepoint, as it is typical for EM data. This works for filenames such as "image-0000" and "image-0001". |
| .*--C(?<C>\d+)--T(?<T>\d+) | One file contains a whole volume. Channel and time point encoded in filenames such as "image--C00--T0000" and "image--C01--T0000" |
| T(?<T>\d+)_(?<C>.*) | One file contains a whole volume. Channel and time point encoded in filenames such as "T0000_gfp" and "T0001_rfp" |
| t(?<T>\d+)_(?<C>.*) | One file contains a whole volume. Same as above but with lower case "t" such as "t0000_gfp" and "t0001_rfp" |
| (?<C>.*)_T(?<T>\d+) | One file contains a whole volume. Channel and time point encoded in filenames such as "gfp_T0000" and "rfp_T0000" |
| (?<C>.*)_(?<T>\d+) | One file contains a whole volume. Channel and time point encoded in filenames such as "gfp_0000" and "rfp_0000". The difference to the example above is that there is no "T" in front of the time points. |
| (?<C>.*)/.*T(?<T>\d+) | One file contains a whole volume. Channels are specified by subfolders and time-points are encoded in filenames such as "gfp/T0000" and "rfp/T0000" |
| .*T(?<T>\d+) | One file contains a whole volume. No channel grouping specified, e.g. "gpf-T0001", "gfo-T0002", etc. (in this case the name of the containing folder will be used as the channel name). |
| .*-(?<T>\d+) | One file contains a whole volume. No channel grouping specified, and no "T" but only a dash "-" as prefix for the time points, e.g. "gfp-00", "gfp-01", etc. (in this case the name of the containing folder will be used as the channel name). |
| .*_(?<T>\d+) | One file contains a whole volume. No channel grouping specified, and just an underscore "_" proceeding the time points, e.g. "Cam_Left_01", "Cam_Left_02", etc. (in this case the name of the containing folder will be used as the channel name). |
| .*_t(?<T>\d+).*_z(?<Z>\d+).*_c(?<C>\d+).* | One file contains a a single plane, such as e.g., "image_t00_z000_c1.tif, image_t00_z000_c2.tif, ...". |
| .*--t(?<T>\d+)--Z(?<Z>\d+)--C(?<C>\d+).* | Works for Leica DSL. One file contains a a single plane, such as e.g., "Position001_Target--t00--Z00--C00.tif". |