Array Generation (per hour)
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- Typically get 3 arrays of 40, 200nm sections per coverslip array.
- That is 120 sections, on 3 coverslips or approximately 24 um in 2.5 hrs.
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AT Tissue Processing - standard processing (1-4 samples)
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- Standard processing of 1-4 samples
- Some samples may be higher due to special needs/processing
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AT Tissue Processing - standard processing (per additional sample)
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- Standard processing fee for each additional sample beyond the base set of 4 samples, processed at the same time
- Some samples may be higher due to special needs/processing
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ATC Technician Time (per hour)
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Bioptech chamber
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Critical Point Dryer - CPD (per run)
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The Tousimis 815, Series A, Critical Point Dryer is a fully automated instrument with a chamber size of 1.25" (ID) and 1.25" (H) and Soter condensor unit to capture waste alcohol and eliminate purge exhaust noise. Samples need to be dehydrated into 100% ethanol before CPD drying with liquid CO2. Samples are mounted (using various custom-made accessories) in ethanol in the CPD chamber and after cooling the chamber, the process will automatically advance through steps of purging, heating till Tousimis equalibrium is reached, followed by gradual bleeding of CO2 gas and venting to ambient pressures.
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Cryo-ultramicrotome (per hour)
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EM TRAINING on SEM
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EM TRAINING on TEM
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Training on TEM or SEM takes 4 hrs, divided into 3hrs (assisted) and 1hr (independent) use
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EMC Technician Time (per hour)
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- Charged per hour
- Instrument time is separate cost
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Fluoro Dish 23mm (small)
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Fluoro Dish 40mm (large)
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FMC Microscope Training & Usage Set-Up
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This is a flat-fee item that covers a training session by CSIF technician for three hours and the setup of a CSIF service account for one microscope instrument. This is a prerequisite for all independent usage of each microscope in the facility.
Please contact CSIF at 650-723-2449 or email microscopy@stanford.edu to discuss your imaging needs and our time availability. After which, CSIF will book time under your name for the training on the specific instrument. Thank you. You can also fill out the email form here.
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FMC Technical Assistance / Consulting (per hour)
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This charge is added whenever extended technician assistance is rendered.
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Freeze substitution (chemicals included; per 2-3 day run)
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Grid Staining (per each additional grid)
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Grid Staining: Uranyl acetate and lead citrate contrast staining ??- charge per each additional grid over first 8 grids
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Grid Staining: Uranyl acetate and lead citrate contrast staining (up to 8 Grids)
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Contrast staining of sections on grids (up to 8) for best morphological analysis: 3.5% Uranyl Acetate in Acetone followed by 2% Lead Citrate.
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More than 8 grids will be at a charge per each additional grid.
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High performance #1.5 cover glass
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Zeiss Schott glass high-performance cover glass #1.5 170+/- 5um (thickness) 18x18mm (LxW). Zeiss # 474030-9000-000.??Required for all super-resolution applications on OMX microscope.??Highly recommended for critical imaging applications, particularly deconvolution. 100/box = 1 each. $5/each for Internal Stanford users
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High Pressure Freezer (per half day; 4 hrs.)
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The Leica EM PACT2 HPF can freeze samples 100 to 200nm thick by 1.5mm in diameter. It can also accomodate 1.2mm round sapphire coverslips which cells can be grown on. (Leica 100nm and 200nm specimen carriers as well as sapphire discs as well as other HPF supplies available at cost)
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Histology Scope: Leica DM2000
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Immuno-EM Cryo Tokuyasu Prep
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2 to 8 samples should be lightly fixed using 2 to 4% EM grade Formaldehyde along with Glutaraldehyde between 0.01 to 0.1% to improve the morphology in 0.1M Sodium Cacodylate or PO4 buffer @ RT 1hr and cut into 1mm3 cubes then placed into 4oC. Fixed cells should be scraped/quenched and washed with buffer then equilibrated with warm 10% gelatin/spun down and pelleted then chilled on ice before cutting into 1mm3 or smaller. They will be embedded equilibrated in 2.3M Sucrose and then frozen on pins for sectioning using the Cryo-ultramicrotome.??
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Immuno-gold Localization (Typical cost. Single antibody/grid on up to 8 grids, including controls)
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??
Typical cost. Single antibody/grid on up to 8 grids, including controls. ??This includes contrast (UA and Pb) staining when appropriate. Additional antibodies, double labeling etc. will increase time and cost.??
NOTES:??Sections should be collected on nickel grids treated with sticky grid solution or Formvar/Carbon coated. Copper grids can be used but uncoated copper grids should not be used.
Sections are mounted on shiny side of grid, all steps below are done with shiny side up.
All incubations should be done in a humidity chamber.
Block, localization and wash are done in ceramic spot plate (Coors).
Reagents for IEM:
PBST: 140 mM NaCl, 3mM KCl, 8mM Na2HPO4, 1.5 mM KH2PO4, 0.05% Tween20, pH7.4
Standard block: PBST, 0.5% (w/v) ovalbumin (Sigma), 0.5 % (w/v) BSA (Sigma)
Sticky grid solution:
4ml 0.5% formvar (Ted Pella, Inc.) (final concentration will be 0.08%)
21ml of a 24:1 (v/v) dichloroethane : chloroform solution
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ImmunoEM Resin embedding
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2 to 8 samples should be lightly fixed using 2 to 4% EM grade Formaldehyde along with Glutaraldehyde between 0.01 to 0.1% to improve the morphology in 0.1M Sodium Cacodylate or PO4 buffer @ RT 1hr and cut into 1mm3 cubes then placed into 4oC. They will be embedded in acrylic resins such as LR White (EMS) or Lowicryl (EMS). These allow for easy storage/trimming/handling of samples at room temperature once embedded.
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Immunolocalizations (1-4 coverslips; per session)
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- up to 4 coverslips at the same time minimum
- separate charge will apply per additional coverslip at same time
- can do multiple antibodies if raised in different organisms (if no cross-reactivity).
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Immunolocalizations (per additional coverslip; same session)
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- Fee for each additional coverslip, beyond the base session charge for first 4 coverslips, processed at the same time
- Separate minimum session charge will include first 4 coverslips
- can do multiple antibodies if raised in different organisms (if no cross-reactivity).
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LSM 510 Confocal, multi-photon
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Materials
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This is used to bill out cost recovery of variable consumable supplies such as specialty coverslips that may not be in existing add-on categories. Please comment and specify what this charge exactly covers per the order.
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Mattek Chamber
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Negative Staining (per additional grid)
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??
NOTE: There is a minimum charge for Negative Staining that includes up to 5 grids.
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Negative Staining - includes reagents (up to 5 Grids)
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??
NOTE: A charge per grid will apply for each additional grid after first five.
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Items needed:
25uM is a good starting point for protein concentration
1% Uranyl Acetate in ddH2O
Grids: Formvar and Carbon coated copper grids (300-400 mesh; Cat#F F300-Cu), glow discharged
DUMONT N4AC Dumoxel tweezers are anti-capillary (Cat# 72870-D www.emsdiasum.com)
Procedure for negative staining:
- Place ~4ul of purified protein on glow discharged 300mesh carbon/formvar coated Cu grids.
- Allow to settle 3 min.
- Wash grids with 3 drops 1% Uranyl Acetate in ddH2O then allow 3rd drop to sit on grid for 1 min.
- Pull off most of drop with filter paper and allow to dry.
- View samples at 120kV on the TEM.
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Nunc Chamber
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OMX Blaze SIM-STORM-Deconvolution
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POC-R coverslip
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SEM Imaging (SEM time plus EM Microscopist time - per hour)
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SEM imaging is done by the staff electron microscopist, using the user/researcher's prepared samples. The user should preferably be present (at least partially) during the first imaging session to discuss and indicate the feautures of interest, and image magnifications required. Data can be downloaded from the SEM-PC on site, or remotely from CSIF servers, or sent to the user through Stanford Box.
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SEM Sample OTO Prep for Serial Section Array (up to 6 samples)
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Samples are aldehyde fixed and resin embedded for ultrathin sectioning similar to TEM analysis, but with additional en bloc staining techniques with heavt metals to improve conductivity of ultrahin sections on glass sides. Slides are carbon coated for improved conductivity, and scanned serially with FESEM to obtain a stack of images for 3D reconstruction.
PROCESS
Fix samples in 4%PFA/2%Glut in 0.1M NaCacodylate Buffer (4h+) Keep overnight or for extended periods of time at 4deg Celsius, fully submerged in fixatives and sealed with parafilm.
Wash in same buffer (2x5min)
OTO:
Post-fix in 1% OsO4 (2hrs) - highly toxic and volatile, keep in vacuum hood
Wash in H2O (3x5min)
Post-fix in TCH: 30min
Wash 3-x5min
Post-fix OsO4: 1hr
Wash 3x5min
Post-fix 2% UranylAcetate: 2hrs (or 1% overnight @ 4C)
Wash 3x H2O
Post-fix Pb-Citrate: 1-2min, as for section staining (closed container, pellet NaOH to absorb CO2) not for 2nd series of embedding
Wash H2O
DEHYDRATE: 30-50-70-90-100-100% EtOH
Dehydrate in 100% Acetonitrile, replace with Acetone (2x) 2nd embedding, prevent curling of membrane
Infiltrate Epon:Acetone 50%[1:1], 66% [2:1] (overnight)100% (4-6hrs) on rotator
Embed in fresh 100% resin, polymerize @ 60oC 2days
Thiocarbohydrazide (1% (wt/vol) aqueous solution) Heat 25 ml of ddH2O on a hot plate to 58oC. Add 0.25 g of TCH to the heated water while stirring until the powder is dissolved, and then leave the solution for 2-3 h; the color will darken. Turn down the heat while stirring. Remove the solution from the hot plate and allow it to cool to room temperature (25oC). Filter using a 0.45 um syringe filter. Store at room temperature to avoid precipitation for up to 1 week
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SEM Sample Prep - Specimen mounting and Sputter Coating (up to 6 samples)
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Prepared specimens (CPD dried and/or cut to size) are mounted on 12 or 25mm aluminum pin stubs using colloidal graphite or Copper tape (or Carbon tabs for Hitachi 3400N VP-SEM only). Strictly NO carbon tabs are allowed in the Zeiss Sigma FESEM.
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For improved conductivity specimens are coated with gold/Palladium (Au/Pd) to a thickness of 50-100Angstroms, using the Denton Desk II sputter-coater. Non-conductive samples can be used uncoated with the Hitachi VP-SEM using low vacuum mode.
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SEM Services: Sample Prep - Fixation and CPD Processing (up to 6 samples)
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Fix tissue (or cells on coverslips, or cells on hydrogels) 4 hrs to overnight in 2% Glutaraldehyde with 4% PFA (Paraformaldehyde) in 0.1M Na Cacodylate Buffer (pH 7.3). Samples should be either cut to appropriate size, grown on 12-22 mm coverslips, or centrifuged to concentrate small particles. Submerge samples in fixatives, close with parafilm, and keep cold (4oC) for 1hr to weeks, before continuing processing. Never allow samples to dry out, or warm to room temperature in fixatives for longer than 1hr. Bacterial samples must be grown to late log pahse (OD~0.6) for sufficient numbers, or grow as biofilm on a suitable surface, or as cell culture on poly-L-lysine coated coverslip. Bacteria can also be fixed in eppendorf tubes, and 100ul aliquots pipetted onto PLL coated coverlips. Vacuum-filtration of bacteria through microporous filters (0.22-0.45um pore size) also allows for retention of small particels, cell clusters or univellular organisms on usable surfaces. Microporous capsules (70-200um pores) that are compatbile with CPD drying can also be used with great success to retain and easily handle small particles during processing.
Wash 5 min in same buffer
Post-fix 1 hr in 1% aqueous OsO4 (Osmium Tetroxide) Highly toxic!! Use in hood!!.
Wash 2x 5 min in mQ H2O
*Dehydrate in increasing ethanol series: 50-70-90-100-100% (10min each).
**CPD (Critical Point Dry) with liquid CO2 with Tousimis Autosamdri 815.
Mount samples with double-sided carbon tape, or Colloidal Graphite, on Aluminum stubs.
Sputter-coat with Pd/Au - 100 Angstrom layer (3-5 min) with the Denton DeskII system in lab.
* Hydrogels and samples in VP-mode, using coolstage control: do not dehydrate, CPD or sputter-coat.
** CPD drying can be replaced by HMDS (Hexamethyldisalazane) drying in conditions where the size, orientation, or other physical parameters are not compatible with CPD conditions. Replace the final 100% ethanol with a 50% solution of HMDS in ethanol (15min), followed by 100% ethanol (2x15min). Remove all HMDS and allow sample to dry overnight in a desiccator.
Supplies needed
Suppliers:
Electron Microscopy Sciences http://www.emsdiasum.com/microscopy/default.aspx
Ted Pella http://www.tedpella.com/
Fixatives:
16% PFA (EMS Cat #15710)
8% Glut (EMS Cat #16020) with
0.2M NaCacodylate (EMS CAT #11652)
Mix equal volumes (1 vial each) of PFA and Glutaraldehyde with 20 ml Buffer for required fix conc
2% OsO4 (EMS Cat #19192) dilute with mQ water to 1% conc.
Colloidal Graphite: Ted Pella #16053
Specimen Mounts: Ted Pella #16111 (1/2 dm slotted head)
Carbon conductive Tape: Ted Pella #16073
Pelco Tabs 12mm: Ted Pella #16084-1
Pelco Tabs 25mm Ted Pella #16084-2
Carbon conductive sheet (x10): Ted Pella #16085-1
Microporous capsules: EMS # 70187 (30 and 78 micron)
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SEM: Hitachi S-3400 VP
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SEM: Zeiss Sigma FESEM
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SP2 Confocal
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SP5 Confocal, multi-photon, FLIM
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SP8 WLL confocal, gSTED, FLIM
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Specimen Processing Reagent Fee - FULL (per processing)
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Specimen Processing Reagent Fee - PARTIAL (per processing)
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Sputter Coater (per run)
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The Denton Desk II sputtering unit is equipped for Gold/Palladium coating and includes a thickness monitor. The secimen chamber can accomodate ten 15mm (D) SEM stubs at a time. Ease of use and reliability are features valuable for use by students from all disciplines.
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TEM JEOL JEM-1400
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TEM of Cells on Coverslips
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Epon Embedding of Cells on Coverslips (typically 4 to 8 samples)(TestJP 8-14-12)
Sample Fixation: (Preferably grown on 12mm round glass or 13mm round Thermanox coverslips)
- Samples fixed in 2 % Glutaraldehyde(8% stock-EM grade) and 4% p-Formaldehyde in 0.1M NaCacodylate (or HEPES, Tris, PO4) buffer pH~7.2 for 20 min @ RT then moved to 4oC for 40 min to a couple of weeks.
Post-Fixation for Epon (Fume hood, Osmium is Toxic!!) All at 4oC
- Fix is then gently replaced with1% OsO4 in ddH2O, Rotated gently and left for 1 hr
- Wash samples briefly 3X each in ddH2O
- Change to 1% Uranyl acetate in ddH2O, stained for 2 hrs to Overnight.
III. Dehydration:
- 50% EtOH, 5 min
- 70% EtOH, 5 min
- 95% EtOH, 10 min (allowed to warn to room temp)
- 100% EtOH, 2X, 15 min each @ RT
- Changed to Acetonitrile for 15 min
Epon* Infiltration: (Use gloves) *Epon = EMbed 812 using 20ml EMbed 812 and 16ml DDSA and 8ml NMA with 1.2ml BDMA
- Change to 1:1 Epon/ Acetonitrile for 1hr
- Change to 2:1 EPON/ Acetonitrile and leave 1 hr
- Replace with 100% Epon 1 hr
- Change to fresh Epon, place labels into beem capsules and fill with fresh resin, put on top of coverslip.
- Polymerize in oven @ 65oC O/N, I usually make about 2 labeled beem capsules/coverslip
- Remove plastic from bottom of coverslip and dissolve glass w/HF (49%) for 20 min
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TEM of Tissue/Cells for morphological analysis
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I. Sample Fixation(2 to 8 samples):
- Samples are usually fixed w/2% glutaraldehyde & 4% paraformaldehyde in 0.1M Sodium Cacodylate buffer, pH 7.4 for 1 hour @Room Temp and cut into blocks ~1mm3. Other buffers can be used: e.g. HEPES or PO4. After fixation samples are then moved to 4oC for immediate processing. Some people have left samples in fix for days to weeks with little change to the morphology.
To enrobe cells in gelatin spin cells down 5 min @ 4kX and wash in buffer 3X: re-suspend cells in warm gelatin, 10% in PBS, for 5 min/spin 5 min @ 4 kX, place on ice 5 minutes then cut into blocks. Cover with cold Osmium(step 2).
II. Post-Fixation @ 4oC(Use Fume hood and gloves, Osmium is toxic)
- Remove fixative and add 1% OsO4 in ddH2O Shake gently and leave for 1 hr @ 4o
- Wash samples 3X, 5 min each w/cold ddH2O
- Change to 1% Uranyl acetate in ddH2O, stain for 2 hr to O/N
III. Dehydration:
- 50% EtOH, 10 min
- 70% EtOH, 10 min
- 95% EtOH, 10 min (allow to warm to room temperature, rest performed at RT)
- 100% EtOH, 2X, 10 min each @ RT
- Acetonitrile 15 min
IV. Epon* Infiltration: (Use gloves):
- Change to 1:1 Acetonitrile/Epon 1hr
- Change to 1:2 Acetonitrile/Epon Overnight
- Change to 100% Epon 2-3 hrs
Place in molds labeled and filled with 100% Epon and allow to settle for 4hr to Overnight (O/N)
- Polymerize in 65oC oven 24hrs
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TEM tomography: Single or Double tilt
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Tomographic reconstruction of 3-D data, based on images acquired as tilted projections, using intermediate voltage electrons interpreted by IMOD which is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, and Quanren Xiong at the Boulder Laboratory for 3-D Electron Microscopy of Cells.
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TEM Ultrastructural Services: Sample Prep - Cryo fixation, freeze substitution (2-8 samples; typical cost)
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(view additional details)
??
***Was originally name:??High Pressure Freezing/Freeze Substitution***
??
Two to Eight samples are typically accepted as one run. The Leica EM PACT2 HPF can freeze samples 100 to 200nm thick by 1.5mm in diameter. It can also accomodate 1.2mm round sapphire coverslips which cells can be grown on. Samples are then freeze substituted/processed into an Eponate for morphological analysis or Acrylic resin for immuno-gold localization.
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TEM Ultrastructural Services: Sample Prep - Microwave-assisted chemical fixation (2-8 samples; typical cost)
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(view additional details)
??
- NOTE: more difficult samples may require additional time and cost.
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TEM Ultrastructural Services: Sample Prep - Standard chemical fixation and resin processing (2-8 samples; typical cost)
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(view additional details)
- Note: more difficult samples may require additional time and cost.
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Ultramicrotome Leica UCT (per hour)
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Obtain Semi-thin (350 to 1000nm thick) and ultrathin (50 to 120nm thick) sections.
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Ultramicrotomy: block trimming (per sample-block, 4 grids)
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??
NOTE: More difficult blocks require additional time/cost.
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Ultramicrotomy: Previously trimmed by EM facility block (per sample-block, 4 grids)
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??
- NOTE: More difficult blocks require additional time/cost.
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Vacuum (Carbon) evaporator (per run)
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The Denton Vacuum Bench Top Turbo (BTT) is a fast, clean, high vacuum bench top evaporator with simple automated operation for evporation or sputtering. It utilizes solid control electronics to control the pumpdown and venting sequences. The pumping package consists of a turbomolecular as well as a mechanical pump. It has a 1kV evaporation power supply for carbon coating, and 4000 volt AC glow, as well as a sputtering module for depositing noble metal. Also, a rotaing and tilting substrate table is included.
OPTIONS:
1. AC GLOW DISCHARGE: All materials exposed to our atmosphere tend to accumulate molecular lauers of oill and water on the surface. These few moleculaar latyers cause the surface to repel water. Carbon fioms so contaminated will cause aqueous solutions to bead rather than to spread over the surface. Contaminated griads will not pick up replicas readily. The AC glow discharge will clean the carbon support films and grids in vacuum of the molecular layers of oil and water.
2. CARBON EVAPORATION SOURCE: The carbon evaporation source is adjustable and is designed to provide carbon fims for support, replication or conduction. Rods 0.04mm (D) are evaporated for 30sec to 2 minutes.
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Work Station #1, 2, 3 Usage
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Data processing computer installed with software for in image data quantification and 3D rendering.
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