eamag/protocols-with-steps huggingface dataset:
TITLE: No Title
AUTHORS: 

[GUIDELINES]
<p><strong>Primers:</strong></p>
<p>rpoC1_103:  CAC TGC GGC AAA TAC AAA CG</p>
<p>rpoC1_360:  TTT CAG GTC CTT GTG GTC AC<br /><br /></p>
<strong><strong>Reaction Mix:<br /></strong></strong>
<table style="width: 400px; height: 150px;">
<tbody>
<tr>
<td>Material</td>
<td>Amt.</td>
<td>Final Conc.</td>
</tr>
<tr>
<td>Water</td>
<td>14.25μl</td>
<td> </td>
</tr>
<tr>
<td>10x Buffer (w/Mg)</td>
<td>2.5μl</td>
<td>=1x</td>
</tr>
<tr>
<td>dNTP mix, 2.5mM each</td>
<td>5.0μl</td>
<td>=500μM ea.</td>
</tr>
<tr>
<td>Primer rpoC1_103, 10µM</td>
<td>0.5μl</td>
<td>=0.2μM</td>
</tr>
<tr>
<td>Primer rpoC1_360, 10mM</td>
<td>0.5μl</td>
<td>=0.2μM</td>
</tr>
<tr>
<td>La-Taq 5U/μl</td>
<td>0.25μl</td>
<td>=0.05U/μl</td>
</tr>
<tr>
<td>DNA (WH7803)</td>
<td>1.0-2.0μl</td>
<td> </td>
</tr>
<tr>
<td> </td>
<td>Total = 25μl</td>
<td> </td>
</tr>
</tbody>
</table>
<br /><br /><strong><strong>Cycling:<br /></strong></strong>
<table style="width: 300px; height: 150px;">
<tbody>
<tr>
<td>95<sup>o</sup>C</td>
<td>5 min</td>
<td> </td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>95<sup>o</sup>C</td>
<td>45 sec</td>
<td rowspan="3"><br />40 cycles</td>
</tr>
<tr>
<td>50<sup>o</sup>C</td>
<td>45 sec</td>
</tr>
<tr>
<td>70<sup>o</sup>C</td>
<td>60 sec</td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>70<sup>o</sup>C</td>
<td>10 min</td>
<td> </td>
</tr>
<tr>
<td>15<sup>o</sup>C</td>
<td>Hold</td>
<td> </td>
</tr>
</tbody>
</table>

[STEPS]
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Protocol for preparing NGFR-mNG2 tagged WM989 A6-G3 melanoma cells for sorting. </p>

[BEFORE_START]
<p>Warm trypsin, media and DPBS. </p>

[STEPS]
?. 
?. 
?. 
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?. 
?. 
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?.
TITLE: Dephosphorylation of 5´-ends of DNA using rSAP (M0371)
AUTHORS: New  England   Biolabs

[DESCRIPTION]
Protocol for Dephosphorylation of 5´-ends of DNA using rSAP (M0371).

[GUIDELINES]
Dephosphorylation of 5´- ends of DNA in Restriction Enzyme Reaction
The phosphate can be added directly into the digestion reaction during or after DNA digestion
rSAP is active in all NEB restriction enzyme buffers
The restriction enzyme should be heat inactivated at the same time as the phosphatase after digest and dephosphorylation
If restriction enzyme(s) cannot be heat inactivated, DNA purification is required before ligation

[STEPS]
1. Prepare a 20 µL reaction as follows:  
DNA1 pmol of DNA ends*CutSmart® Buffer (10X)2 µlrSAP1 unitH2O, purifiedto 20 µl**
 
 
 

2. Incubate at 37 °C for 30 min.
3. Stop reaction by heat-inactivation at 65 °C for 5 min.
TITLE: Tissue Fixation | HubMAP | JHU-TMC
AUTHORS: Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Miklhail James, Sashank Reddy, Denis Wirtz

[DESCRIPTION]
 First and most important - the original tissue sample must be of good quality. Factors such as warm 
ischemic time, the time delay between tissue excision and fixation, etc. are important. Ideally, tissues 
should be acquired as close to still being viable as possible, and put into fixative as soon as possible
following excision. Delays lead to cell death, autolysis, and loss of tissue and cell integrity with concomitant 
losses of immunostaining (e.g., due to proteolysis of the antigen). If acquiring animal tissues, consider 
performing perfusion fixation before organ/tissue removal if it is an option

[STEPS]
SECTION: Tissue Fixation
1. Tissue is harvested using our protocol (Tissue Harvesting Protocol)
SECTION: Tissue Fixation
4. The rate of penetration of formaldehyde depends on the size of the biopsy. Trimming is often required to facilitate fixation. Tissues placed in the tissue cassettes should be no thicker than 3-4mm because the interior of a specimen may not become fully fixed, or significant autolysis can occur.

Reference - Oncology Tissue and Imaging Services – at Johns Hopkins (jhu.edu)
SECTION: Tissue Trimming
5. Trimming also helps remove unwanted parts of the biopsy such as excessive fat and traumatized
edges.
SECTION: Tissue Trimming
6. Label tissue cassette with sample ID with pencil
SECTION: Tissue Trimming
7. Place the trimmed tissue in cassette
SECTION: Tissue Trimming
8. Place cassettes back into the histology container
SECTION: Tissue fixation (continue)
9. Refill 10% NBF into the container and leave for 12~48 hours at room temperature.

Use plenty of fixative. The general rule is to use at least 15 volume equivalents of formalin per volume 
of tissue. A higher formalin-to-tissue ratio certainly won't hurt, and just requires a larger container. 
Formalin is relatively cheap, so don’t skimp on this step.

Recommended reading - Active monitoring of formaldehyde diffusion
into histological tissues with digital acoustic interferometry - PMC (nih.gov)
SECTION: Tissue fixation (continue)
11. Pour the formalin into an “excess formalin” waste container in the hood.
SECTION: Tissue fixation (continue)
12. Rince the cassettes in the histology container with 1x PBS 
SECTION: Tissue fixation (continue)
13. Drain and refill the PBS. Leave the cassette submerged in PBS and store at 4 degree C
until processing.
SECTION: Tissue fixation (continue)
14. Properly fixed tissue can be stored in PBS up to a week.
SECTION: Tissue Fixation
2. We submerge the biopsy in the histology container prefilled with 10% NBF for fixation
SECTION: Tissue Fixation
3. Minimizing the warm ischemic time is critical. The time delay between tissue excision and fixation is detrimental to further analysis.

Note on the effect of delay to formalin fixation - Delay to
formalin fixation effect on breast biomarkers - PubMed (nih.gov)

SECTION: Tissue fixation (continue)
10. Gentle agitation of the tissue in the formalin during fixation maximize diffusion and reduce the poor local fixation.
TITLE: Phage DNA extraction with Monarch kit and digestion to single nucleosides 
AUTHORS: Atanas Radkov, Adair  Borges

[DESCRIPTION]
This protocol details high-molecular-weight DNA extraction from bacteriophages using the NEB Monarch HMW DNA Extraction Kit for Tissue. Following DNA extraction, DNA is digested down to single nucleosides using the NEB Nucleoside Digestion Mix.

[STEPS]
SECTION: Nucleoside digestion
10. Use a Nucleoside Digestion Mix (NEB - M0649S) to digest 1 µg of DNA. Each reaction should contain 1 µL of Nucleoside Digestion Mix and 2 µL of 10× Nucleoside Digestion Mix buffer.
SECTION: Nucleoside digestion
11. Perform reactions in 20 µL total volume and incubate at 37 °C for 1 h, followed by enzyme inactivation at 80 °C for 15 min. Keep digested samples at 4 °C until ready for downstream use or analysis.
SECTION: Phage DNA extraction (using NEB Monarch HMW DNA Extraction Kit for Tissue)
2. Aliquot 300 µL of concentrated phage into a 1.5 mL Eppendorf tube. This will be used for DNA harvest with the NEB Monarch HMW DNA Extraction Kit for Tissue (NEB T3060L), using the modifications for bacteriophages suggested by NEB in their extremely helpful technical note. 

 
SECTION: Phage DNA extraction (using NEB Monarch HMW DNA Extraction Kit for Tissue)
3. Add 300 µL HMW gDNA tissue lysis buffer and 20 µL proteinase K to the aliquoted phage. Incubate at 56 °C for 45 minutes on a Thermomixer at 250 rpm. If you only have a static heat block, vortex every 10 min.
SECTION: Phage DNA extraction (using NEB Monarch HMW DNA Extraction Kit for Tissue)
4. Add 300 µL of protein separation solution with gentle mixing. Spin down at 16 × g  for 10 min.
SECTION: Phage DNA extraction (using NEB Monarch HMW DNA Extraction Kit for Tissue)
5. Move aqueous layer (around 900 µL, organic is around ~50 µL at bottom) to a fresh 1.5 mL Eppendorf tube. Add two DNA capture beads to aqueous layer. Then add 550 µL of isopropanol to the tube to begin precipitation.
SECTION: Phage DNA extraction (using NEB Monarch HMW DNA Extraction Kit for Tissue)
6. Put the Eppendorf tube onto a rotator set at the slowest speed, and rotate for 5 min to bind DNA to beads. If you do not have a rotator, do 25 slow and gentle manual inversions.
SECTION: Phage DNA extraction (using NEB Monarch HMW DNA Extraction Kit for Tissue)
7. After DNA binding, pipette off the liquid from the beads and wash the beads twice with 500 µL of DNA wash buffer.
SECTION: Phage DNA extraction (using NEB Monarch HMW DNA Extraction Kit for Tissue)
8. Move the beads to the bead retainer, and pulse very quickly in a bench-top centrifuge to remove any residual liquid from the beads.
SECTION: Phage DNA extraction (using NEB Monarch HMW DNA Extraction Kit for Tissue)
9. Quickly move the beads to a new clean tube, and add 100 µL of Elution buffer. Elute at 56 °C for 5 min. After elution, transfer the eluate to a fresh tube and Nanodrop.
SECTION: Degradation of host nucleic acids
1. To degrade any non-encapsulated nucleic acids, treat the concentrated phage lysate with 10 µg/mL RNase A (NEB T3018) and 10 µg/mL DNase I (NEB M0303). Digest for 1 h at room temperature or 4 °C overnight. Store phage at 4 °C.
TITLE: ROS staining
AUTHORS: Magdalena Julkowska

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol adapted from Shin et al., 2005 and Orman-Ligeza et al. 2016 (citing Shin)</div></div>

[STEPS]
?. [Transfer the seedlings from agar plates into nutrient solution containing DCF-DA (50 uM) for 30 min. Preferably in darkness as DCF-DA is light sensitive]
?. [wash with medium without DCF-DA and image fluorescence microscopy (460–500 nm bandpass excitation. Emission of 510– 560 nm bandpass]
?. [wash with medium without DCF-DA and image fluorescence microscopy (460–500 nm bandpass excitation. Emission of 510– 560 nm bandpass]
TITLE: Preparation of Recording ACSF (artificial cerebrospinal fluid) for slice electrophysiology
AUTHORS: Sarthak M. Singhal, thnasko

[DESCRIPTION]
Hnasko lab- preparation of Recording ACSF
Recording ACSF is used for incubating brain slices during cell-attached or whole-cell electrophysiological recordings of neurons.

[STEPS]
1. Prepare 10X stock solution.
1.1. Composition of 1 L of 10X Recording ACSF (in mM): 1250 NaCl, 25 KCl, 12 NaH2PO4, 125 d-glucose, 20 CaCl2 and 20 MgSO4.

1.2. Composition of 1 L of 10X Recording ACSF (in g): 73.05 NaCl, 1.86 KCl, 1.44 NaH2PO4, 22.52 d-glucose, 2.94 CaCl2 and 4.93 MgSO4.

2. Dissolve all salts in 1 L of ddH2O to make 10X stock solution of Recording ACSF.

3. Dilute 10X solution to 1X for use in experiments.
3.1. Dilute 100 mL of 10X solution to ~ 800 mL with ddH2O and add (in mM): 26 NaHCO3; (in g): 2.18 NaHCO3.

3.2. Add ddH2O to final volume of 1 L.

4. Bubble the solution with carbogen (95% O2 5% CO2) for ~10 min.
5. After bubbling, measure and adjust pH of solution to ~ pH 7.3 with 12 N HCl (<1 ml).
6. Refrigerate until use.
TITLE: No Title
AUTHORS: 

[GUIDELINES]
<strong>Materials:</strong> <br />- 10 place filter manifold<br /> - Towers (chilled overnight @ 4C) <br />- 5% (w/v) Trichloroacetic acid (TCA) (chilled overnight @ 4C) Usually 1L is enough for a single time series set <br />- 32 15ml centrifuge tubes <br />- Pump <br />- Scintillation vials and fluid (UltimaGold) <br />- Lab supplies<br /><br /><strong>Map:<br /><br /><a href="https://s3.amazonaws.com/pr-journal/uyc2xe.jpg" target="_blank"><img src="https://s3.amazonaws.com/pr-journal/uyc2xe.jpg" alt="" /></a><br /></strong>

[STEPS]
?. 
?. 
?. 
?. 
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?. 
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?. 
?. 
?. 
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?. 
?. 
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TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<div title="Page 4">
<div>
<div>
<p><span style="font-size: 9.000000pt; font-family: 'AdvHelv_R'; color: rgb(13.725000%, 12.157000%, 12.549000%);">Experimental set up for BONCAT coupled with fluorophore addition via copper (I)- catalysed azide-alkyne cycloaddition (i.e., click chemistry) to detect the the transfer of HPG, a methionine analogue, from newly synthesized proteins in host cells to their viruses during lytic infection. </span></p>
</div>
</div>
</div>

[STEPS]
?. 
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TITLE: Drosophila melanogaster inoculation with Bd
AUTHORS: Tatum S Katz, Alyssa Byer, Renwei Chen

[DESCRIPTION]
Methods to inoculate D. melanogaster with Batrachochytrium dendrobatidis. 

For manuscript Drosophila melanogaster is a possible vector of Batrachochytrium dendrobatidis under review at PLOS One.

[STEPS]
SECTION: Protocol
1. Plate 0.5ml of treatment (10^6 zsps per fly or DI water) onto each agar plate
2. Allow plates to dry so that no water is puddled on the surface
3. Place 10 flies onto each plate
4. Seal plates with parafilm and incubate at room temperature for 24 hours
5. Transfer flies into fly vials (keeping all flies from the same plate together in the same vial)
6. Euthanize flies in the freezer at desired time point (within 5 days). Or, use the living inoculated flies for another protocol
7. If you want to test the difference between washed and unwashed flies, you may wash a group of up to 5 flies at a time in PBS buffer using 500ul per fly prior to DNA extraction.
8. Inoculated flies are now ready for DNA extraction or other methods.
TITLE: bHEV genotpying RT-PCR
AUTHORS: Siu Fung Ho

[DESCRIPTION]
bHEV genotpying RT-PCR

[STEPS]
SECTION: Polyermase Chain Reaction
14. Setup mastermix in a 1.5 mL eppendorf tube. The following amounts are for a single reaction

Component                                Volume
2x Reaction Mix               25 µL   
Forward Primer 10 μM     2 µL
Reverse Primer 10 μM     2 µL
Nuclease-free water       16 µL 
Total                                 50 µL

 

SECTION: Polyermase Chain Reaction
15. Add 5 µL template cDNA to the PCR tubes.

 

SECTION: Polyermase Chain Reaction
16. Gently mix contents of each tube by pipetting and spin down.
SECTION: Polyermase Chain Reaction
17. Program the following PCR cycles into the thermal cycler.

Step                                         Temperature             Time                   Cycles
Reverse transcription     50 °C     10 min            1
Inactivation                     98 °C     2 min            1
Denaturation                   98 °C     10 s            10    
Annealing                        50 °C     10 s            10
Extension                        72 °C     30 s            10
Denaturation                   98 °C     10 s            30
Annealing                        60 °C     10 s            30
Extension                        72 °C     30 s            30
Final extension               72 °C     5 min            1

SECTION: Reverse Transcription
2. Make up the primer annealing master mix in a 2ml Eppendorf. Per sample volumes:

Component                                    Volume
dNTPs 10mM                         1 µL
Reverse Primer 2mM             1 µL
Nuclease-free water        Up to 13 µL

SECTION: Reverse Transcription
8. Vortex and briefly centrifuge the 5x SSIV Buffer.
SECTION: Reverse Transcription
5. Mix and briefly centrifuge.
SECTION: Reverse Transcription
7. Incubate on ice for at least 1 minute.
SECTION: Reverse Transcription
6. Heat the RNA-primer mix at 65°C for 5 minutes.
SECTION: Reverse Transcription
1. Pre-warm the 5x SSIV buffer to RT
SECTION: Reverse Transcription
3. Divide13 µL of master mix between reaction tubes.

SECTION: Reverse Transcription
4. Add up to 5 µgRNA template to reaction tubes.

SECTION: Reverse Transcription
9. Make up the RT master mix in a 2ml Eppendorf. Per reaction volumes:

Component                                                       Volume
5x SSIV Buffer                                      4 µL
DTT 100 μM                                          1 µL
RNase Inhibitor                                     1 µL
Reverse Transcriptase (200 U/μL)      1 µL

 

SECTION: Reverse Transcription
10. Mix and briefly centrifuge RT master mix
SECTION: Reverse Transcription
11. Add 7 µL of RT master mix to annealed RNA

 


SECTION: Reverse Transcription
12. Incubate the combined reaction mixture at 50°C for 10 minutes
SECTION: Reverse Transcription
13. Inactivate the reaction by incubating it at 80°C for 10 minutes. During this incubation, PCR mastermix can be setup (next step).
TITLE: Orange peel | Chitosan | Hemp
AUTHORS: Jil A Berenblum   Phoenix Lai   Esther Chang   Anna Lu

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Orange peel | Chitosan | Hemp</span></div></div>

[STEPS]
?. Remove the peel from an orange(we used Citrus Sinensis Navel Oranges from Florida). While the peel is still fresh, blend it into small granules. The size of the granules can affect the characteristics of the end material.
?. In a bowl, combine the Hemp Protein Powder , Gluten , and granulated Orange Peel   Mix the ingredients together until they become evenly distributed. The mixture should resemble a light brown powder with visible orange specs. Set this bowl aside.
56 g
56 g
90 g
?. In a separate bowl, stir together the water and vinegar . The water and vinegar should be at room temperature before they are combined.
180 mL
?. Incorporate the chitosan   into the water/ vinegar solution in small parts. Be sure to add the chitosan slowly while constantly mixing so that the chitosan can dissolve evenly into the solution.
13.5 g
?. Slowly add the chitosan/vinegar/water  solution into the bowl containing Hemp Protein Powder/ Gluten/ Orange peel.  Bring the mixture together with a silicone spatula as the solution is added. Switch to hand kneading the material if the Chitosan and the gluten become too sticky for the spatula. Stop mixing when the material resembles a brown dough like consistency.
45 mL
?. Press the material into a mold or onto a cooking sheet. Place in the oven at 200F until dry or leave the mixture to air dry for a few days.
?. As part of a biodesign research group, we reimagined where waste products could be used. This material looks to live harmoniously with the lifetime of product use, so by using all natural ingredients, it biodegrades sooner rather than later.  This also creates a collaboration between different industries and people as the ingredients are usually discarded. Essentially building a material to create with nature. Through this material, we were able to build strong vessels that can be sanded, oiled, and shaped through molding or high power tools such as the bandsaw and drill.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
This protocol provides a method to predict phage community diversity using the algorithm PHACCS. Sequencing of viral communities often results in a high percent of unknown reads, largely due to our incomplete reference databases. To address this unknown factor of viromes, the algorithm PHACCS (PHAge Communities from Contig Spectra) was developed to predict virus community alpha diversity without the use of taxonomic references. Based on the methods from the following publication:<br /><br />Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." <em>mBio</em> 6.5 (2015): e01578-15.<br /><br /><br />

[BEFORE_START]
Perl scripts and other supplemental information available at:<br /><br /><a href="https://figshare.com/articles/The_Human_Skin_dsDNA_Virome_Topographical_and_Temporal_Diversity_Genetic_Enrichment_and_Dynamic_Associations_with_the_Host_Microbiome/1281248" target="_blank">https://figshare.com/articles/The_Human_Skin_dsDNA_Virome_Topographical_and_Temporal_Diversity_Genetic_Enrichment_and_Dynamic_Associations_with_the_Host_Microbiome/1281248</a>

[GUIDELINES]
<strong>Required Software:</strong><br />
<ul>
<li>PHACCS-1.1.3</li>
<li>Circonspect-0.2.6</li>
<li>GAAS-0.17</li>
<li>Octave-3.8.1</li>
</ul>
<strong>Relevent Files</strong><br /><br />Output:<br />
<ul>
<li>Alpha_diversity/virus_and_phage_acc_numbers.txt</li>
<li>Alpha_diversity/PHACCS_results_all.txt</li>
</ul>
R scripts: <a href="https://www.protocols.io/view/Script-R5-Virome-Alpha-Diversity-eimbcc6" target="_blank">R5</a>, <a href="https://www.protocols.io/view/Script-R6-Virome-Beta-Diversity-einbcde" target="_blank">R6</a>, <a href="https://www.protocols.io/view/Script-R10-Whole-Metagenome-Beta-Diversity-ejebcje" target="_blank">R10</a>

[STEPS]
?. 
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TITLE: Transformation of the chlorarachniophyte Amorphochlora amoebiformis by electroporation
AUTHORS: Kodai Fukuba, Liz Cooney, Nick Irwin, Patrick J. Keeling, Yoshihisa Hirakawa

[STEPS]
?. [Plasmid preparation]
Propagate plasmid DNA (pLaRGfp or its derivatives, such as pLaR182+GFP) in the Escherichia coli strain DH5α.
?. [Plasmid preparation]
Purify plasmid DNA from 200 mL culture of E. coli by a Qiagen Plasmid Maxi Kit (Qiagen).
?. [Plasmid preparation]
Adjust plasmid DNA concentration to 3-5 µg/µL with distilled water.
?. [Cell culture]
Culture Amorphochlora amoebiformis (CCMP2058) cells in 500 mL Erlenmeyer flasks containing 200 mL ESM medium at 20°C under white illumination (50-80 μmol photons·m−2·s−1) on a 14:10 hours light:dark cycle for a week.
?. [Cell culture]
After decanting medium, resuspend cells adhered to the bottom of flasks by gentile pipetting with 2 to 3 mL ESM medium (use a glass pipette). Approximately 4×107cells can be obtained from a flask.
?. [Electroporation]
Harvest a total of 5×106 cells by centrifugation at 2,000 g for 5 sec (use a mini centrifuge).
?. [Electroporation]
Resuspend cell pellet in 100 µL of Gene Pulser electroporation buffer (Bio-Rad) with 10 µL of plasmid DNA at the room temperature.
?. [Electroporation]
Transfer cell solution into electroporation cuvette with 0.2 cm gap (Bio-Rad).
?. [Electroporation]
Electroporate cells with a 25 ms square wave pulse at 120 V using Gene Pulser Xcell Electroporation System.
?. [Electroporation]
Add 0.9 mL fresh ESM medium to cuvette immediately after electroporation.
?. [Electroporation]
Transfer cells to glass bottom well plate/petri dish, and add an appropriate volume of ESM medium.
?. [Electroporation]
Incubate cells for 24 hours before observation of GFP fluorescence.
TITLE: Processing of Radial K-space DW-MRI Data
AUTHORS: Miguelrj  , Hee  Kwon Song, Stephen  Pickup, Mamtaaryagupta  , Rong  Zhou

[DESCRIPTION]
The protocol includes reconstruction of diffusion weighted images from radial k-space data and using a 3-parameter fit to derive metrics of ADC and kurtosis index.

[STEPS]
1. Image reconstruction

Radially acquired diffusion-weighted images (DWIs) are reconstructed using the following steps:

Apply zero-order phase correction to each radial spoke using the average phase offset at the center slice of the lowest b-value image
Zerofill k-space by a factor of 2 to double field of view
Multiply signal of each point by its respective area on a Voronoi diagram of the points (including added zerofill points) in k-space
Re-grid each radially defined point to its nearest Cartesian coordinate using its Kaiser-Besel index
Apply Fourier transform to now Cartesian-defined k-space


This process can be easily conducted using the CIRP Python library [link]. Once the library is installed, the DWI reconstruction class can be imported using
 

To instantiate the class, the image dimensions, b-values, readout resolution, and number of views must be defined: