documents:130327cellcognition
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
documents:130327cellcognition [2013/03/27 15:39] – [a small tip for OSX] kota | documents:130327cellcognition [2016/05/24 12:46] (current) – external edit 127.0.0.1 | ||
---|---|---|---|
Line 1: | Line 1: | ||
+ | ====== CellCognition ====== | ||
+ | ===== custom name schemes ===== | ||
+ | |||
+ | For importing image series, specific name scheme, based on python regex but with some restrictions with obligatory fields and so on, must be adde to the file ~/ | ||
+ | |||
+ | **A small tip for OSX** | ||
+ | |||
+ | By the way, Christoph Schiklenk pointed out that in MacOSX, ~/Library is hidden in the Finder. That's true, so what you need to do is the following. Open Terminal, then do the following command (just copy the whole line and then return) to open the file: | ||
+ | < | ||
+ | open -a TextEdit ~/ | ||
+ | </ | ||
+ | |||
+ | ==== example 1: Fiji/ ImageJ output ==== | ||
+ | |||
+ | File name should be for example images_P0_C0_Z0_T0000.tif and all files should be placed under a single directory per series. | ||
+ | |||
+ | < | ||
+ | [ImageJ_Only_TimePoints Working] | ||
+ | # Simple numbered tiff files, such as the one exported by " | ||
+ | # in ImageJ e.g. " | ||
+ | # underscore (_) should be immediately before the frame numbering. | ||
+ | # http:// | ||
+ | file_extensions = .tiff .tif | ||
+ | regex_subdirectories = ^[^_].* | ||
+ | regex_filename_substr = (.+?)\. | ||
+ | regex_dimensions = ^.+? | ||
+ | timestamps_from_file = mtime | ||
+ | </ | ||
+ | |||
+ | ==== example 2: Fiji/ ImageJ output ==== | ||
+ | |||
+ | This scheme was written for Fiji output ([File > Save As > Image Sequence]) | ||
+ | |||
+ | Another contributions from Christoph Schiklenk @ EMBL Heidelberg. | ||
+ | Naming scheme with CellCog 1.2.5 on Mountain Lion. | ||
+ | |||
+ | < | ||
+ | [EMBL_Fiji_Position] | ||
+ | file_extensions = .tiff .tif | ||
+ | regex_subdirectories = ^[^_].* | ||
+ | regex_filename_substr = (.+?)\. | ||
+ | regex_dimensions = _p(? | ||
+ | </ | ||
+ | |||
+ | ==== example 3: Fiji/ ImageJ output ==== | ||
+ | |||
+ | This scheme was written for Fiji output ([File > Save As > Image Sequence]) | ||
+ | |||
+ | Another contributions from Christoph Schiklenk @ EMBL Heidelberg. | ||
+ | Naming scheme with CellCog 1.2.5 on Mountain Lion. | ||
+ | |||
+ | < | ||
+ | [EMBL_Fiji_SubwellPosition] | ||
+ | file_extensions = .tiff .tif | ||
+ | regex_subdirectories = ^[^_].* | ||
+ | regex_filename_substr = (.+?)\. | ||
+ | regex_dimensions = .*w(? | ||
+ | </ | ||
+ | |||
+ | ==== example 4: Zeiss output ==== | ||
+ | |||
+ | For importing data of Zeiss780, single channel. | ||
+ | (naming of the entry is not proper at the moment) | ||
+ | |||
+ | Contribution from Yin Cai @ EMBL Heidelberg | ||
+ | |||
+ | < | ||
+ | [EMBL_ScanR_OME_WPZT_test] | ||
+ | file_extensions = .tiff .tif .ome.tif | ||
+ | regex_subdirectories = ^[^_].* | ||
+ | regex_filename_substr = (.+?\.) | ||
+ | regex_dimensions = | ||
+ | .*? | ||
+ | timestamps_from_file = mtime | ||
+ | allow_subfolder = data | ||
+ | </ | ||
+ | |||
+ | ==== example 5: CellBase ==== | ||
+ | |||
+ | Contribution from Andreas Boni, EMBL Heidelberg. | ||
+ | |||
+ | " | ||
+ | CellBase subfolder and naming scheme" | ||
+ | < | ||
+ | [EMBL_ScanR_OME_Andreabis] | ||
+ | file_extensions = .tiff .tif .ome.tif | ||
+ | regex_subdirectories = ^[^_].* | ||
+ | regex_filename_substr = (.+?\.) | ||
+ | # | ||
+ | .*? | ||
+ | regex_dimensions = | ||
+ | .*? | ||
+ | timestamps_from_file = mtime | ||
+ | allow_subfolder = data | ||
+ | </ | ||
+ | |||
+ |
documents/130327cellcognition.txt · Last modified: 2016/05/24 12:46 by 127.0.0.1