2 - motivate fluorescence microscopy
3 - explain its drawbacks (usually only 5s exposure without changing biology)
6 # /data/floh-junk/0117/final/kielhorn-ssi2011_0120.pdf
7 - distance between consecutive lenses always sum of both focal lengths
8 - source is output of integrator rod
9 - if mirrors are flat, image of source on B1
10 - if mirrors are tilted, light no longer passes through the aperture
11 - mma is imaged into bfp, tilted mirrors are dark there
12 #+CAPTION: Thin lens model of the optical system. L{1..5} lenses, M{1,2,3} mirrors, B1 adjustable aperture, PBS polarizing beam splitter, D1 dichroic beam splitter
14 #+CAPTION: Photograph and drawing of the system.
16 - give examples how it can be used to improve illumination
17 for c. elegans samples
19 - first order in b1 is at an angle FIXME
20 - aperture stop should have FIXME diameter
21 - ideally half orders should be blocked
22 - this leads to an image diameter on the lcos, in the sample plane FIXME
23 ** light homogenization
24 - fiber illuminated under an angle
25 - rotating microlenses with 5 degree divergence FIXME
26 - 250mm light tunnel, needs to be rectangular for mixing effect,
27 caustics in round tunnels prevent homogenization FIXME paper
28 ** Other approaches of light control
29 - other approaches in the literature:
32 - CLEM, feedback loop paper
34 - comparison of the different approaches
35 - SPIM and HiLo only do angular control
36 - SPIM doesn't seem to have any real disadvantage, its sectioning (1 .. 3 um?)
37 isn't as good as CLEM but usually sufficient for embryos
38 - CLEM only works with coherent light and can do good sectioning with a confocal
39 - Levoy spatial resolution is limited and fixed (depending on what
40 microlenses he uses), our system has high spatial resolution but
41 we shouldn't make use of it otherwise the angular control
43 - Levoy is the only one, that can instantaneously illuminate
44 different regions of the sample with different angles. We (and
45 Holo and Kino) could multiplex in time, though.
46 - Holo is an approach that we tried using a different phase
47 gratings in the image plane.
48 - Kino would be an approach where several phase SLM would act as a
49 Kinoform element and redistribute light from dark areas into the
50 bright ones (hasn't been tried to my knowledge).
53 | Approach | Angular | Spatial | Sectioning | Throughput | Incoherent | Advantage | Disadvantage |
54 |----------+---------+---------+------------+------------+------------+------------------+-----------------|
55 | SPIM | ++ | - | + | ++ | + | even drosophilia | sample mount |
56 | HiLo | ++ | - | o | o ? | + | | untilt |
57 | CLEM | - | ++ | ++ | ++ | - | | |
58 | Levoy | + | + | - .. o ? | o | ++ | | adaptive |
59 | Holo | + | + | - | - | -- | only one SLM | discrete angles |
60 | Kino | + | + | - | + or ++ ? | -- | | |
61 | Our | + | ++ | - .. ++ ? | - | - | | adaptive |
63 ** The electronic system
64 - explain how devices are synchronized
65 *** Liquid crystal on Silicon Display
66 - maybe describe how it works (but there isn't much information available)
67 *** Micro mirror array
68 #+CAPTION: MMA images, left: SEM image, middle: optical reflective , right: exaggerated rendering of how a 8x8 checker pattern would be displayed on the device
70 - 256x256 mirrors with 16 um pitch
71 - angle continously adjustable from 0 to 2 degree (blazed condition
72 for full visible range)
73 - use fourier filter to convert into intensity device
74 - Fraunhofer contrast measurement
75 - tilt all mirrors, keep frame flat
76 - measure intensity at three areas in the filtered image
77 - plot intensity versus deflection, find minimum
79 ** The optimization system
80 *** Illumination optimization via Raytracing
81 *** Expected improvement with controlled light exposure (lack of Simulation will make that hard to write)
82 *** Expected improvement with angular illumination
83 *** Experimental results
86 ** Simulating the microscope
87 *** Raytracing through immersion objective
88 *** On locating nuclei
89 *** On tracking nuclei
90 *** Angular point spread function
91 *** Comparison of widefield and spatio-angular illumination
92 src/memi-sim-austria/*.m
93 *** Optimization of illumination
95 compare performance of different cameras (SNR agains light
96 intensity), support our choice of camera
97 ** On measuring light intensity in the focal plane
98 ** On the choice of the objective
99 explain our choice of the objective
100 ** Controlling the micro-mirror array
101 ** Synchronizing electronics by microcontroller
102 ** Preparing C. elegans embryos for imaging
104 * List of all documents I have written parts of
105 ** Simulation of the Spatio-Angular Illumination Microscope
106 - ./cyberpower/safed/0806/doc/control.pdf
108 - ray-sphere intersection model
115 ** Equidistant spiral sampling
116 - ./cyberpower/safed/0914/spiral/spiral.pdf
117 - idea to sample a round region with a 1d array
119 - ./uffz/safed/0628/drawing.pdf
121 ** D6.7 Fully integrated and operational system
124 - synchronization (only a note that i use V-SYNC now)
127 - microscope control with z and OpenGL, IPMS-ffi
128 - raytracer for the whole memi system
129 ** Spatioangular Microscopy
130 - ./torben/safed/0123/anim2.pdf
132 - first raycasting images
133 - polarization theory to describe DIC images
134 - construction of nomarski
136 ** Description of the Hologram experiment (Draft)
137 - ./torben/safed/0525/hologram.pdf
138 ** D6.8a Integration of initial MMA optics
139 - ./torben/safed/0708/D8pt6a_mk3_sc1_rh1.pdf
140 - images of MMA and LCoS
141 - I later had to replace the MMA image (pixel defects)
143 ** Simple Raytracer in Common Lisp
144 - ./torben/safed/0821/lens/doc/build/lens.pdf
148 - immersion objective
150 - ./torben/safed/0321/talk/kielhorn-21month-meeting.pdf
154 - Nomarski construction
158 ** 9month-report: Spatio-angular controlled light exposure microscopy
159 - ./torben/safed/y2009/0411/inhalt.pdf
160 - intro fluorescence microscopy with Jablonski
162 - CLEM, SPIM, HILO, OPM (Dunsby)
163 - oblique illumination with MMA
165 - 2000Amos protein localization
166 - 1999Amos book review
167 - 2006Bao cell lineage tracking
169 - 2007Botcherby aberration free refocusing
170 - 2008Bozinovic (Mertz) sectioned endomicroscopy
171 - 2006Corsi c elegans guide
174 - 2004e2v datasheet ccd
175 - 1996Fisher quantum yield
178 - 2006Haken Quantenchemie
179 - 1983Hamai quantum yield
180 - 2006Heintzmann structured illumination
181 - 2008Hirvonen thesis
183 - 2004Holoeye LC-R2500 manual and spec
185 - 2008Konopka variable angle
186 - 2004Krueger diffractive optics
187 - 2008Machu D6.2 biological paradigm
189 - Photometrics datasheet
190 - 2007Stuurman micromanager
193 - 2008Vogelsang blinking
195 - ./torben/safed/y2009/0807/clempam.pdf
196 - simulate apotome, hilo and 2-grating method
198 - 2008Lim speckle sectioning
200 - 2009Santos sectioning through fibre bundle
201 ** Measuring EM excess noise factor
202 - ./torben/safed/y2009/0414/excess-noise-factor.pdf
203 - compare the noise in the two readout registers for the same image
204 ** Holoeye Phase Only Characterization
205 - ./torben/safed/y2009/0512/kielhorn_heo.pdf
206 - where I first observed timing issues
208 - ./torben/safed/y2009/0427/mm_mk3.pdf
209 - documentation how to write device adapters
210 - camera driver for bluefox
212 - some thoughts on using graphics cards with sync input
213 ** Improved setup for testing the DIC idea
214 - ./torben/safed/1104/kielhorn_dic.pdf
215 - short talk with 8 pages
216 - data for the two shift directions
218 - ./torben/safed/0417/uni.pdf
219 - construction of refraction through Wollaston
220 - only ray directions for now
221 - thats where I found the error from the company
222 - needs propagation distance to be a useful simulation
223 - intensities of reflected and transmitted beams are potentially in there
225 - the papers I used are attached
229 - 1960Nomarski (patent)
230 ** D6.5 Holography Method
231 - ./torben/safed/0624/doc/D6pt5_sc1_mk7_rh1_js1.pdf
232 ** Getting more with less (Randall Retreat poster)
233 - ./torben/safed/0831/doc/build/retreat2010.pdf
235 - Susan sectioning / Controlled Light exposure
237 ** /home/martin/ftp.ipms.fraunhofer.de/MEMI_PPR_Y2_Deliverables_and_Milestones/
238 *** MMA evaluation version
239 - MEMI_PPR_Y2_D6_10_v2_0.pdf
241 - white light interferometer image
242 - first images of fourier plane
243 - very crude angular illumination experiment
244 - ref: Fraunhofer manual
245 *** Report on the DIC Experiments
246 - MEMI_PPR_Y2_D6_06_v2_0.pdf
247 - deflection curve fit
248 - compare piston and tilt mirror
249 - compare the two shear directions
250 - measure split angle of nomarski
251 - refraction at a birefringent surface
253 - DIC gray image generator
254 - raytracing construction with conic functions
255 - ref: 1960Nomarski_patent`, (1996Goodman, 1991Saleh)
256 ** Monday PhD meeting
257 - /data/safe-with-time/torben/safed/0301/kielhorn-phd.pdf
259 ** Preliminary Installation Manual for MEMI system
260 - /data/floh/0219/memi-alignment/align.pdf
261 - just before I visited France
262 ** Analysis of improvements of CLEM with angular control
263 - /data/floh/0207/D6p8a_sc2_rh1_mk2.pdf
264 - written by Susan based on my description
265 - shows angular illumination on beads
266 - describes model generation
267 - describes ray model for objective
268 - describes sphere-intersection model with the orange images
269 - describes projection model but not for extended in-focus parts
270 - references: 2008Hwang, (2005Wolf, 2006Celis)
271 ** Spatio-angular Microscopy
272 - /data/floh/0117/final/kielhorn-ssi2011_0120.pdf
273 - for proceedings of smart systems integration conference
274 - introduction, description of MMA, description of light path
275 - /home/martin/0315/ssi_poster.pdf
276 - smooth projection model
277 - widefield vs. spatio-angular
278 - code: generate thin lens model
279 - references: 2004Huisken, 2008Tokunaga, 2007Hoebe, 2010Berndt, 2010Schmidt
281 * Interesting other Documents
283 *** D6.2 Physical and biological test samples for MEMI
284 - torben/safed/0320/D6pt2_final.pdf
285 - phototoxicity, H2B-GFP
286 - many papers referenced
287 *** Analysis of improvement of CLEM over standard microscopy
288 - MEMI_PPR_Y2_D6_04A_v1_1.pdf
290 - noise estimation by comparison with 2D polynomial fit
291 - S/N improved with CLEM in sectioned image
293 - 1998Murray Performance eval
295 - 2008Hoebe CLEM quantitative
297 * Not directly related
298 ** Journal Club talks
299 ** Phase retrieval in Hubble Space Telescope
300 - ./torben/safed/0308/kielhorn_jc-fienup-phase-retrieval.pdf
302 ** Optoacoustic tomography
303 - ./torben/safed/y2009/0727/journal_club.pdf