Initial import of rev. 258 from the now-obsolote

#######################################################################

#

# Cross platform CMake configure script

#

#######################################################################

cmake_minimum_required(VERSION 2.6)

# set the compilation way

SET(CMAKE_VERBOSE_MAKEFILE ON CACHE STRING

	          "Tracing the compilation process" FORCE)

#

# set the debug/release version

#

OPTION(DEBUG_VERSION "Shall I add debug information?" ON)

IF (DEBUG_VERSION)

		  SET(CMAKE_BUILD_TYPE "RELEASE" CACHE STATIC "" FORCE)

	ADD_DEFINITIONS(-DGTGEN_DEBUG -Wall)

ELSE (DEBUG_VERSION)

   SET(CMAKE_BUILD_TYPE "RELEASE" CACHE STATIC "" FORCE)

	ADD_DEFINITIONS(-Wall)

ENDIF (DEBUG_VERSION)

#

# options

#

OPTION (BUILD_STATIC "Shall I prepare the gtgen-ng as a static executable?" OFF)

OPTION (SHOW_TERRITORIES "Shall I also output images with labelled territories?" OFF)

OPTION (SHOW_CENTRES "Shall I also incorporate chromocentres into output phantom images?" OFF)

OPTION (SHOW_NUCLEI "Shall I also output images with nuclei masks?" ON)

OPTION (SAVE_FINAL "Shall I also generate final images from phantom images?" ON)

OPTION (USE_REAL_PSF "Shall I use real PSF for final images (slower!!!)?" OFF)

OPTION (HIGH_SNR "Shall I generate final images of higher SNR (not applied if real PSF is used)?" ON)

OPTION (SAVE_TIFFS "Shall I save 3D TIFF images rather than ICS images?" OFF)

OPTION (SHOW_FLOWFIELDS "Shall I also output flow field images?" OFF)

OPTION (DO_RIGID_MOTION "Shall I include rigid movement (translation plus rotation) of cells into the simulation?" ON)

OPTION (DO_NONRIGID_MOTION "Shall I include non-rigid movement (smooth shape deformation) of cells into the simulation?" ON)

OPTION (DO_FLAT_2DMOTION "Shall I prevent cells from movement along z-axis?" OFF)

OPTION (EVENTS_SYNCHRONIZED "Shall I force more-or-less strong synchronization of cell mitoses?" OFF)

OPTION (DO_MULTITHREADING "Shall I do parallel computing (based on threads) if available?" ON)

OPTION(ISOTROPIC_GROUND_TRUTH "Shall we keep the GT image to the isotropic" OFF)

OPTION(PHOTOBLEACHING "Shall I imitate photobleaching of fluorochrome" ON)

IF (SHOW_TERRITORIES)

    ADD_DEFINITIONS(-DGTGEN_WITH_TERRITORIES)

ENDIF (SHOW_TERRITORIES)

IF (SHOW_CENTRES)

    ADD_DEFINITIONS(-DGTGEN_WITH_CHRCENTRESINPHANTHOMS)

ENDIF (SHOW_CENTRES)

IF (SHOW_NUCLEI)

    ADD_DEFINITIONS(-DGTGEN_WITH_NUCLEIMASKS)

ENDIF (SHOW_NUCLEI)

IF (SAVE_FINAL)

    ADD_DEFINITIONS(-DGTGEN_WITH_FINALIMAGES)

ENDIF (SAVE_FINAL)

IF (USE_REAL_PSF)

    ADD_DEFINITIONS(-DGTGEN_WITH_REAL_PSF)

ENDIF (USE_REAL_PSF)	

IF (HIGH_SNR)

    ADD_DEFINITIONS(-DGTGEN_WITH_HIGHSNR)

ENDIF (HIGH_SNR)

IF (SAVE_TIFFS)

    ADD_DEFINITIONS(-DGTGEN_WITH_TIFFS)

ENDIF (SAVE_TIFFS)

IF (SHOW_FLOWFIELDS)

    ADD_DEFINITIONS(-DGTGEN_WITH_FLOWFIELDS)

ENDIF (SHOW_FLOWFIELDS)

IF (DO_RIGID_MOTION)

    ADD_DEFINITIONS(-DGTGEN_WITH_RIGIDMOTION)

ENDIF (DO_RIGID_MOTION)

IF (DO_NONRIGID_MOTION)

    ADD_DEFINITIONS(-DGTGEN_WITH_NONRIGIDMOTION)

ENDIF (DO_NONRIGID_MOTION)

IF (DO_FLAT_2DMOTION)

    ADD_DEFINITIONS(-DGTGEN_WITH_JUST2DTRANSLATIONS)

ENDIF (DO_FLAT_2DMOTION)

IF (EVENTS_SYNCHRONIZED)

    ADD_DEFINITIONS(-DGTGEN_WITH_STRONGSYNCHRONIZATION)

ENDIF (EVENTS_SYNCHRONIZED)

IF (DO_MULTITHREADING)

    ADD_DEFINITIONS(-DGTGEN_WITH_MULTITHREADING)

ENDIF (DO_MULTITHREADING)

IF (ISOTROPIC_GROUND_TRUTH)

    ADD_DEFINITIONS(-DGTGEN_WITH_ISOTROPIC_GT)

ENDIF (ISOTROPIC_GROUND_TRUTH)

IF (PHOTOBLEACHING)

		  ADD_DEFINITIONS(-DGTGEN_WITH_PHOTOBLEACHING)

ENDIF (PHOTOBLEACHING)

#

# documentation stuff

#

OPTION (DOCUMENTATION "Shall I generate documentation (requires Doxygen)?" OFF)

IF (DOCUMENTATION)

	FIND_PROGRAM(DOXYGEN_PROGRAM doxygen PATHS ${BIN_DIRS}

	  DOC "Path to the Doxygen documentation program.")

	ADD_CUSTOM_TARGET(docs

		${CMAKE_COMMAND} -E chdir ${CMAKE_SOURCE_DIR}

		${DOXYGEN_PROGRAM} Doxyfile)

ENDIF (DOCUMENTATION)

#

# collect all the source files

#

SET (SRCS 

		  src/main.cpp

		  src/dots.cpp

		  src/molecule.cpp

		  src/scheduler.cpp 

		  src/cell.cpp 

		  src/cell_01_Prophase.cpp 

		  src/cell_02_Metaphase.cpp 

		  src/cell_03_Anaphase.cpp 

		  src/cell_04_Telophase.cpp 

		  src/cell_05_Cytokinesis.cpp 

		  src/cell_06_G1Phase.cpp

		  src/cell_07_SPhase.cpp

		  src/cell_08_G2Phase.cpp

		  src/cellChr.cpp

		  src/cellScm.cpp

		  src/toolbox/rnd_generators.cpp 

		  src/toolbox/flowfields.cpp 

		  src/toolbox/collisions.cpp

		  src/toolbox/deformations.cpp

		  src/toolbox/perlin.cpp

		  src/toolbox/shape_rendering.cpp

		  src/toolbox/rnd_generators.cpp

		  src/toolbox/bp_lists.cpp 

		  src/toolbox/cell_movement.cpp

		  src/toolbox/finalpreview.cpp

		  src/toolbox/user_abort.cpp

		  src/toolbox/hungarian/Assignment.cpp

		  src/toolbox/hungarian/Hungarian.cpp

		  src/toolbox/hungarian/BipartiteGraph.cpp

    )

# build the final target

ADD_EXECUTABLE(gtgen-ng 		${SRCS})

ADD_EXECUTABLE(remove_label	src/toolbox/tracks/remove_label.cpp)

ADD_EXECUTABLE(merge_images	src/toolbox/tracks/merge_images.cpp)

ADD_EXECUTABLE(correct_tracks	src/toolbox/tracks/correct_tracks.cpp)

ADD_EXECUTABLE(extract_flow	src/toolbox/motion/extract_flow.cpp)

ADD_EXECUTABLE(getMax			tools/getMax.cpp)

#

# dependencies...

#

INCLUDE_DIRECTORIES(/usr/local/include)

IF (BUILD_STATIC)

	SET(CMAKE_FIND_LIBRARY_SUFFIXES ".a")

   SET(CMAKE_CXX_FLAGS "-static")

ELSE (BUILD_STATIC)

	SET(CMAKE_FIND_LIBRARY_SUFFIXES ".so")

	# dynamic i3dalgo uses the f2c library for which

	# the following tweak must be here

	SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Xlinker -defsym -Xlinker MAIN__=main")

ENDIF (BUILD_STATIC)

# GSL - gnu scientific library

FIND_PATH(INC_GSL "gsl/gsl_randist.h")

INCLUDE_DIRECTORIES(${INC_GSL})

FIND_LIBRARY(LIB_GSL "gsl")

SET(LIBS ${LIBS} ${LIB_GSL})

# I3D - image 3D library

FIND_PATH(INC_I3D "i3d/image3d.h")

INCLUDE_DIRECTORIES(${INC_I3D} ${INC_I3D}/i3d)

FIND_LIBRARY(LIB_I3DCORE "i3dcore")

FIND_LIBRARY(LIB_I3DALGO "i3dalgo")

SET(LIBS ${LIBS} ${LIB_I3DALGO} ${LIB_I3DCORE})

# dynamic linker

FIND_LIBRARY(LIB_DL "dl")

SET(LIBS ${LIBS} ${LIB_DL})

# IniParser -- tool for parsing INI files (part of CytoPacq project)

FIND_PATH(INC_INIPARSER "ini/iniparser.h")

INCLUDE_DIRECTORIES(${INC_INIPARSER})

FIND_LIBRARY(LIB_INIPARSER "iniparser")

SET(LIBS ${LIBS} ${LIB_INIPARSER})

# CytoPacq - static simulator & its features

FIND_PATH(INC_CYTOPACQ "cytopacq/cytogen.h")

INCLUDE_DIRECTORIES(${INC_CYTOPACQ})

FIND_LIBRARY(LIB_CYTOGEN "cytogen")

FIND_LIBRARY(LIB_OPTIGEN "optigen")

FIND_LIBRARY(LIB_ACQUIGEN "acquigen")

SET(LIBS ${LIBS} ${LIB_CYTOGEN} ${LIB_OPTIGEN} ${LIB_ACQUIGEN})

IF (BUILD_STATIC)

		  # pridat knihovny, ktere vyzaduje i3d-cko

		  FIND_LIBRARY(LIB_LAPACK lapack)

		  FIND_LIBRARY(LIB_BLAS blas)

		  FIND_LIBRARY(LIB_GFORTRAN gfortran PATHS /usr/lib/gcc/x86_64-pc-linux-gnu/4.6.3)

		  SET(LIBS ${LIBS} ${LIB_LAPACK} ${LIB_BLAS} ${LIB_GFORTRAN})

		  FIND_LIBRARY(LIB_TIFF tiff)

		  FIND_LIBRARY(LIB_JPEG jpeg)

		  FIND_LIBRARY(LIB_ICS ics)

		  FIND_LIBRARY(LIB_PNG png)

		  FIND_LIBRARY(LIB_HDF5_HL hdf5_hl)

		  FIND_LIBRARY(LIB_HDF5 hdf5) 

		  SET(LIBS ${LIBS} ${LIB_TIFF} ${LIB_JPEG} ${LIB_ICS}

		  					 ${LIB_PNG} ${LIB_HDF5} ${LIB_HDF5_HL})

		  FIND_LIBRARY(LIB_LZMA lzma)

		  FIND_LIBRARY(LIB_Z z)

		  SET(LIBS ${LIBS} ${LIB_LZMA} ${LIB_Z})

		  FIND_LIBRARY(LIB_FFTW_SINGLE_THREADS fftw3f_threads)

		  FIND_LIBRARY(LIB_FFTW_SINGLE fftw3f)

		  FIND_LIBRARY(LIB_FFTW_DOUBLE_THREADS fftw3_threads)

		  FIND_LIBRARY(LIB_FFTW_DOUBLE fftw3)

		  FIND_LIBRARY(LIB_FFTW_LDOUBLE_THREADS fftw3l_threads)

		  FIND_LIBRARY(LIB_FFTW_LDOUBLE fftw3l)

		  SET(LIBS ${LIBS} ${LIB_FFTW_SINGLE_THREADS}

					 ${LIB_FFTW_SINGLE}

					 ${LIB_FFTW_DOUBLE_THREADS}

					 ${LIB_FFTW_DOUBLE}

					 ${LIB_FFTW_LDOUBLE_THREADS}

					 ${LIB_FFTW_LDOUBLE})

		  FIND_LIBRARY(LIB_GSL gsl)

		  FIND_LIBRARY(LIB_GOMP gomp PATHS /usr/lib/gcc/x86_64-pc-linux-gnu/4.6.3)

		  FIND_LIBRARY(LIB_PTHREAD pthread)

		  SET(LIBS ${LIBS} ${LIB_GSL} ${LIB_GOMP} ${LIB_PTHREAD})

			SET_TARGET_PROPERTIES(gtgen-ng PROPERTIES LINK_SEARCH_START_STATIC ON)

			SET_TARGET_PROPERTIES(remove_label PROPERTIES LINK_SEARCH_START_STATIC ON)

			SET_TARGET_PROPERTIES(merge_images PROPERTIES LINK_SEARCH_START_STATIC ON)

			SET_TARGET_PROPERTIES(correct_tracks PROPERTIES LINK_SEARCH_START_STATIC ON)

			SET_TARGET_PROPERTIES(extract_flow PROPERTIES LINK_SEARCH_START_STATIC ON)

			SET_TARGET_PROPERTIES(getMax PROPERTIES LINK_SEARCH_START_STATIC ON)

ENDIF (BUILD_STATIC)

# link the target with the required libraries

TARGET_LINK_LIBRARIES(gtgen-ng ${LIBS})

TARGET_LINK_LIBRARIES(correct_tracks ${LIBS})

TARGET_LINK_LIBRARIES(remove_label ${LIBS})

TARGET_LINK_LIBRARIES(merge_images ${LIBS})

TARGET_LINK_LIBRARIES(extract_flow ${LIBS})

TARGET_LINK_LIBRARIES(getMax ${LIBS})

code cleanup:

- pridat stredniky za vsechny REPORT makra (i DEBUG_REPORT)

- vyuzit pridaneho Scheduler::sceneOffset a nahradim jim vsude, kde se offset doluje ze sceneMasks[i]

- projit vsechny new konstrukce a podivat se, jestli tam potom take dela delete

- IDs pri 8bit maskach se vypisuji jako znaky (chybi pretypovani)

pridat cestu k pnArrayCache souboru do INI souboru, chceme to??

non-rigid: obecne spise male, casteji (nyni 2x, mozna 3-4x) udelat velke non-rigid

non-rigid: zachovava sice vicemene objem, ale vubec neresi tvar

customizace na kontretni data

proverit jak se zachovava trackovaci informace u bodu (a chrCentres) behem cytokineze atd.

lepsi reprezentaci nebo renderovani bunky: masky vice uzavirat

udelat treba watchdog na tvar masky: abychom neztraceli izolovane body, aby maska byla jakoby vice kompaktni, hladký tvar

(ale musi to svihat, renderovani je nevytezovanejsi funkce)

nepujdou nejake operace udelat vektorove? aby se omezilo preskakovani mezi seznamem bodu a rastrovanim

02-metaphase nema jeste uplne natvrdo asynchronizaci..., prokontrolovat i ostatni: anafaze taky ne

poladit objemy, aby G1 delala vetsi rozptyl vysledku, ktery se musi empricky zjistit z jiz vygenerovanych bunek

rust asi nebude uplne linearni.. promyslet s tim, ze pocet bunek se mnozi exponencialne a bunka ma fixni objem

mozna vice zajistit, aby po deleni byl soucet objemu dcer vicemene podobny objemu matky... nyni to umi dost kolisat

pohyb bunky: zda se, alespon u tomour cells, ze bunka je bud mesenchymalni nebo amoeboidni. Prve je v podstate

druh pohybu, kdy je bunka relativne protazena (je tam recognized polarity) a funguje takovy to protrusion

and retraction a bunka se posouva ve smeru polarity. Druhe je v podstate druh pohybu, kdy je bunka spise kulata

a vice menavkoidni pomerne nevypocitatelne/nepredvidatelne, volne se promenuje kdekoliv (blebbing).

lepsi rotace, vice ve stylu nahlych pootoceni (podobne jako non-rigid), hodnoty odtusit ze soucasnych modes

aby se snizil pocet neuspesnych simulaci napr. due to "Can't find any way out of here", muzeme

zkusit udelat backup bunky pred tim, nez se ze Scheduleru zavola jeji DoNextPhase(), a chytat jeste

ve Scheduleru vyjimky, kdyz se chyti vyjimka, bunka se obnovi z te backup kopie a zkusi se DoNextPhase()

zavolat znovu, takhle treba max 3x nez se to definitivne vzda, na konci se v kazdem pripade zrusi ten backup

|

to vyzaduje, aby bunky vzdy uklidili lokalne vytvorene heapove alokace predtim nez zavolaji throw()

|

tohle reseni zachovava atomicitu fazove funkce bunky, kdy ta fce jede dale primocare bez nejakych

zadnich vratek a moznosti navratu k nejakym checkpointum atd.

||

alternativne muzeme restartovat stejnou bunkou s nejakou SetDelay()

||

alternativne muzeme zkusit preplanovat a "tahnout" jinou bunkou

sliby pro ISBI2014:

What we have:

- photobleaching based on real measurements

- uneven illumination based on real measurements

- the use of real PSF

What we plan:

- increased motility of cells

- improved cell motion model

- less synchronized mitotic events

- more cells

(the last two points should provide more tracking events)

(podle videi se da vyrazne zhorsit casovy krok a zbrutalnit pohyby;

 vyraznost zmeny tvaru, zda se mi, nezavisi od velikosti cas. kroku)

- jeste muzeme: cas od casu globalne posunout scenu, asi v ramci postprocessingu

konkretni ukoly pro Vlada pro ISBI2014:

- jinak rotace a sunuti bunky - vektorove pole pro toceni vc. deformaci

- predelat dle toho globalni pohyby

- pokud hezka pole, upustit od non-rigid deformaci dosavadnim zpusobem

- restarty atom. operaci

- nastavit vice bunek, akcnejsi pohyby

- poladit komety: nevzdavaji se snadno, behaji hloubeji

- Karel - poladit velikosti rustu atd.

- vice vlaknovy model

- vyrabeni 2D + plus omezeni ve 2D pohybech

{

ZRUSENO A NECHANO NA POSTPROCESSING:

scheduler bude mit VOI, do ktereho bude exportovat vysledek generovani

je ale potreba detekovat, kdy bunka zmizi z VOI a upravit tracks.txt

a je potreba detekovat, kdy se bunka objevi ve VOI, poprosit ji o nové VOI a upravit tracks.txt

detekce se dá například udělat tak, že se bude pamatovat jaké IDs byly viděny naposledy

ODLOZENO, PROTOZE TO ZATIM NEPREDSTAVUJE PROBLEM:

Comety muzou vybihat ze svych lokalnich masek, upravit AllocateAndZeroNewMask()

(ale ta potom bude vyrabet velky obrazky a vse se tak hodne zpomali)

}

;

;--------------- characteristics of one 'universal' cell ----------------

;

[cell]

; Should be 23 for humans.

chromosome count = 23

; Lengths of phases of cell cycle

; (in percents)

;

; Well, they sum up to only 95% (not 100%) and that is because

; there is Cell::SetDelay() executed after cytokinesis, which

; delays, that is, lengthen/enlarges, the budget of the G1 phase

; by 0% to 10%  (with mean of 5%) of the cell cycle length.

; So the \e durationOfG1Phase ranges, in fact, from 45% to 55%

; yielding new total of 95% to 105% (with mean at 100%).

;

; times correspond to literature

duration of G1 phase = 45.0

duration of S phase = 30.0

duration of G2 phase = 15.0

duration of prophase = 1.25

duration of metaphase = 2.85

duration of anaphase = 0.25

duration of telophase = 0.325

duration of cytokinesis = 0.325

;

;testing:

;durationOfG1Phase = 1.0

;durationOfSPhase = 1.0

;durationOfG2Phase = 1.0

;durationOfProphase = 1.0

;durationOfMetaphase = 1.0

;durationOfAnaphase = 1.0

;durationOfTelophase = 20.0

;durationOfCytokinesis = 1.0

;

;

; amount of fluorophore molecules filling the nucleus interior

; (in percents)

;

coverage = 300.0

;

; The average diameter of standard cell (in microns)

;

cell diameter = 7.0

;

; A diameter of nucleolus (in microns)

;

nucleolus diameter = 1.4

;

; How far a cell can normally move between frames (in microns)

;

; When setting this value, take into account how many

; frames are used to sample cell cycle, which correlates

; with time delay between acquisition of frames in real

; situation

;

; Default value is based on our observation that a cell

; moves 1.5-2.0um/frame if time-sampling is 9.5min/frame,

; and about 1um/frame if time-sampling is 5min/frame. Thus,

; both cases yield "average" velocities of 0.184um/min and 0.2um/min.

; We use 0.19um/min and 23.75hrs/cycle.

;

; This value must not be greater than cellLookDistance.

;

; Erik data:

; cellMagnitudeOfMovementPerFrame = 0.6 

;

; short sequences

cell magnitude of movement per frame = 0.4 

;

; How far a cell can move between frames (in microns) if the cell is cometing.

; Refer to the type StateOfComet for details about cometing.

;

comet cell magnitude of movement per frame = 0.5

;

; maximum magnitude of vectors used for usual and occuring-most-of-the-time

; non-rigid deformation of cells (in microns)

;

; short sequence:

cell nonrigid deformation = 0.15

;

; maximum magnitude of vectors used for "strong" non-rigid

; deformation of cells (in microns); this deformation typically

; happens just occasionally and, unlike the deformations driven

; with the cellNonRigidDeformation constant, one usually notices it

;

; observed from Erik's data:

; cellNonRigidStrongDeformation = 1.0

;

; short sequence:

cell nonrigid strong deformation = 0.7

;

; Should or shouldn't non-rigid deformations (if available) be done

; in every frame. It is good to disable them when noFramesPerCellCycle

; is more than 60.

;

; Erik's data:

; const bool cellSparseNonRigidDeformations=true;

;

; short sequences:

cell sparse nonrigid deformations = false

;

; How far a cell can "see" when it is trying to move

; to region with lower density of cells (in microns).

;

; The higher the value is, the greater outlook a cell has

; and the higher chance it flows into less dense region (

; and the higher time demand for the simulation :-).

;

; This value must not be less than cellMagnitudeOfMovementPerFrame.

;

; Erik data:

; cellLookDistance = 1.1f*cellMagnitudeOfMovementPerFrame; 

;

; short sequences:

cell look distance = 0.6

; two presets available: "Erik data" vs. "short sequences"

;

; Default (average) number of frames per cell cycle

;

; Observation: 

; 150 frames/cycle gives 9.5min/frame provided cycle lasts 23.75 hours.

; 285 frames/cycle gives 5min/frame provided cycle lasts 23.75 hours.

;

; Erik data:

; noFramesPerCellCycle = 150

; short sequences:

number of frames per cell cycle = 50

; Eva data:

; noFramesPerCellCycle = 280; 

intensity of nonspecific staining = 2

;

;-------------- characteristics of scheduler -------------------

;

[scheduler]

;

; Number of initial cells put into the process

;

number of initial cells = 10

;

; A constant that defines which slice from fully _ISOtropic_ 3D image

; should be used for spatiotemporal image. The spatiotemporal images

; are created from the ISOtropic images before these are anisotropically

; resampled.

;

slice of interest = 60

;

;---------------- optical system --------------------------------------

;

;

[objective]

name = Zeiss 63x/1.40 Oil DIC (new)

magnification = 63

[microscope]

name = Zeiss S100

magnification = 0.859

[microscope adapter]

magnification = 1

[confocal unit]

name = Atto CARV

magnification = 1

[confocal unit adapter]

magnification = 1

[psf]

;experimentaly measured point spread function

;corresponding to the selected components

;location = /mnt/gryf/COMMON/DATA/PSF/2013-01-30_1_1_9_0_2_0_0_1_0_0_0_0_11_14.ics

location = 2013-01-30_1_1_9_0_2_0_0_1_0_0_0_0_11_14.ics

;location = /home/xulman/gryfCOMMON/DATA/PSF/2013-01-30_1_1_9_0_2_0_0_1_0_0_0_0_11_14.ics

[light source]

;experimentaly measured quadratic surface of uneven illumination

;corresponding to the selected components

b1 = 0.8507717563

b2 = 0.0003232258

b3 = 0.0002796816

b4 = -0.0000000193

b5 = -0.0000003282

b6 = -0.0000002623

[fluorophore]

photobleaching rate = 0.003

[camera]

name = Micromax 1300-YHS

pixel size = 6.7

dynamic range = 12

grid = (1300,1030)

baseline = 550

ADC gain = 6

ADC offset = 0

read out noise = 25

dark current = 0.1

full well depth = 18000

[acquisition]

time = 5000

dynamic range usage = 40

[table]

z step = 0.2

[voi]

; size and shift in microns

size = (110,110,12)

shift = (0,0)

[subpixel precision]

level = 1