====== 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  ~/Library/Application Support/CellCognition[version number]/name_scheme.ini. Below are some example (and working) entries.

**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:
<code>
open -a TextEdit ~/Library/Application\ Support/CellCognition1.2.5/naming_schemas.ini
</code>
 
==== 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. 

<code>
[ImageJ_Only_TimePoints Working]
# Simple numbered tiff files, such as the one exported by "SaveAs > Image Sequence"
# in ImageJ e.g. "images_P0_C0_Z0_T0000.tif". Assumes 2D time series, no channels.
# underscore (_) should be immediately before the frame numbering. 
# http://cmci.embl.de
file_extensions = .tiff .tif
regex_subdirectories = ^[^_].*
regex_filename_substr = (.+?)\.
regex_dimensions = ^.+?_P(?P<position>.+)_C(?P<channel>.+)_Z(?P<zslice>\d+)_T(?P<time>\d+)
timestamps_from_file = mtime
</code>

==== 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.

<code>
[EMBL_Fiji_Position]
file_extensions = .tiff .tif
regex_subdirectories = ^[^_].*
regex_filename_substr = (.+?)\.
regex_dimensions = _p(?P<position>\d+)_t(?P<time>\d+)_z(?P<zslice>\d+)_c(?P<channel>\d+)
</code>

==== 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.

<code>
[EMBL_Fiji_SubwellPosition]
file_extensions = .tiff .tif
regex_subdirectories = ^[^_].*
regex_filename_substr = (.+?)\.
regex_dimensions = .*w(?P<subwell>\d+)_p(?P<position>\d+)_t(?P<time>\d+)_z(?P<zslice>\d+)_c(?P<channel>\d+)
</code>

==== 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

<code>
[EMBL_ScanR_OME_WPZT_test]
file_extensions = .tiff .tif .ome.tif
regex_subdirectories = ^[^_].*
regex_filename_substr = (.+?\.)
regex_dimensions =
.*?--W(?P<well>\d+)--P(?P<subwell>\d+)--Z(?P<zslice>\d+)--T(?P<time>\d+)\.
timestamps_from_file = mtime
allow_subfolder = data
</code>

==== example 5: CellBase ====

Contribution from Andreas Boni, EMBL Heidelberg. 

"basically the same of Yin for Zeiss after conversion based on
CellBase subfolder and naming scheme"
<code>
[EMBL_ScanR_OME_Andreabis]
file_extensions = .tiff .tif .ome.tif
regex_subdirectories = ^[^_].*
regex_filename_substr = (.+?\.)
#regex_dimensions =
.*?--W(?P<well>\d+)--P(?P<subwell>\d+)--Z(?P<zslice>\d+)--T(?P<time>\d+)--(?P<channel>.+?)\.
regex_dimensions =
.*?--(?P<position>.+)--P(?P<subwell>\d+)--T(?P<time>\d+)--Z(?P<zslice>\d+)--(?P<channel>.+?)\.
timestamps_from_file = mtime
allow_subfolder = data
</code>