Archive for the ‘tools’ Category

Altoids tins are autoclavable

July 11, 2012

Last night I decided to autoclave (sterilization process that uses 125 C steam) the tin container that Altoids mints come in in order to see if they would survive the temperature/pressure.   The tins looked the exact same inside and outside after autoclaving.

It is not a huge surprize the tins survived – they are metal after all.  My actual intent in doing this was to use the tins as petri-dishes – which is why I needed to sterilize them in an autoclave.  But while the autoclaving of the tins went flawlessly, my media preparation failed miserably.  I tried to make some growth media with red wine, body-builder amino-acid supplements, sugar, and agar-agar (edit: FYI I boiled off most of the alcohol).  For whatever reason the media would not harden.  I will try again sometime after this week because I will be going to the TAM conference in Vegas this year!

Altoids (before)

Altoids (before)

Altoids inside (before)

Altoids inside (before)

As far as using these containers as petri-dishes goes – my only concern is the hinge.  It appears that when closed, the lid covers the hinge hole and should keep the innards sterile.  Until I get the media to harden I will not know if that is a problem or not.

Even if the tins fail to work as petri-dishes (metal could have unforeseen issues for micro-organisms), they may work out as containers for auto-claving parts or components.

Altoids (after)

Altoids (after)


How to add a second deck to an orbital shaker or rocker.

August 26, 2011

Orbital shakers are awesome – they keep fluids homogenous (and thusly remove the need for one to stir the liquid) and are fun to stare at.  The orbital shaker has a cousin called  a rocker which, as is implied, tilt side to side in a rocking motion.  Most labs have one of the two machines, but what if you need more than one?  This was the case for my lab.

The lab kept running out of space on the orbital shaker and this was obviously annoying.  But what was more annoying was the fact that these machines cost about a grand and if an accessory that adds a second deck is available, it usually costs a couple hundred bucks.  All of this led me to building a second deck out of common items from the hardware store.  The guide below should help you through the process I used.

What you need:

    • Tools
      • Orbital shaker or rocker
      • Drill
      • Drill bits
        • <1/4” bit, for drilling pilot hole
        • 1/4” bit
      • PVC pipe utter or hacksaw [PVC cutter is best]
      • 1/4” socket and socket wrench [for tightening bolts]
      • Marking pen
      • Tape measure
    • Consumables
      • Material for deck (plexiglass, plastic, wood, scrap materials, metal, etc.  whatever you can get)
      • PVC fittings (1/2″)
        • 3-way pieces (4) [more about this in the guide below]
        • adapter for 3-way piece (4) [more about this in the guide below]
        • end cap (4)
      • PVC pipe (1/2″)
      • PVC glue [attaching deck to frame]
      • Superglue [alternative to PVC glue and used on bolts]
      • 1/4” Bolts (4)
      • 1/4” Nuts (4)
      • 1/4” Washers (8)
      • Non-slip drawer and shelf liner


Before and after

Drill a pilot hole into the center of all PVC end cap pieces.  Next drill a 1/4″ hole through the center of each end cap.  The result should be something similar to the picture below.  If the photo below looks…odd, that is because my camera is ancient and I had to use software to fix the darkness.

End caps with holes in them.

Remove the friction mat from the orbital shaker.  For all of the shakers that I have encountered, the mats were never attached to the machine – they simply sit in the platform.

Remove the platform from the orbital shaker base.  In my case this required the removal of four phillips head screws.

Remove the platform from the machine BEFORE drilling holes.

Without thinking I drilled into the platform while it was still attached to the shaker (note the holes in the image above).  I did not damage or mar anything as I put thick plastic in-between the orbiting platform and the base of the unit.  But even with this in mind, it always be best to detach the platform from the base of the unit before drilling.

With the platform removed from the base of the unit, use the four PVC end caps as guides for drawing circles where the holes are destined to be.

As with the PVC fittings, start by drilling pilot holes into each of the marked spaces and then follow up with the full sized bit.

Drilled hole.

Attach the end caps to the platform by using the bolts, nuts and washers.  The order for the pieces is, starting from the bottom side of the platform; bolt head, washer, platform, PVC end cap, washer, nut, end of the bolt.  Cut quater circles or triangles into the four corners of the old rubber friction mat so that there is room for it and the bolted end caps on the platform.  Reattach the platform to the base of the orbital shaker.

Close up of a bolted end cap.

All four end caps bolted to the orbiting platform.

For cutting the PVC pipe I recommend a PVC pipe cutter (see picture below).  These make cutting pipe super easy and make less mess than hacksaws (sawing vs. cutting).

PVC pipe cutter

Assemble the 3-way pieces if needed.  If a the 3-way piece as depicted below was used, there is nothing to assemble.  I could only find a 3-way piece that has 2 smooth holes for pipe and 1 threaded hole.  This is not a problem because an adapter that goes from 1/2″ threaded to 1/2″ pipe is available.

Non-threaded 3-way PVC pipe fitting.

Decide how tall you want the second deck to be and cut 4 equal lengths of PVC pipe.  Take into consideration both the height supplied by the fittings and how much pipe rests inside of a fitting.  Depending on the size of the orbital shaker being modified, cut lengths of pvc pipe that will connect all four 3-way pieces to one-another.  Assemble all of the fittings and lengths of pipe together on the rocker to see if it all fits together and to check if everything is level and squared.

Orbital shaker and frame.

Remove the frame work (all lengths of PVC pipe and 3-way fittings, but not the end caps) from the rocker.  It is now time to attach the deck.  Depending on what material is available, chose the best option for attaching it to the frame.  I had some scrap plastic from a junk-heap that I attached to the frame using PVC glue.  This ought to hold well because PVC glue partially melts plastic surfaces together to make a stronger attachment point.  Some alternative ideas for attaching the deck include drilling holes for nuts and bolts, superglue, caulking, and drilling holes for threading metal wire.

I neglected to photograph the gluing process of the deck.  As a result I only have the photo below to illustrate how I attached the deck.

PVC glue was added to the corners and the deck was placed on top.

Once the deck is dry, mount the frame and deck to the platform of the orbital shaker.

Gather some non-slip drawer and shelf liner, cut it to the size of the deck, and place it on the deck. I was able to pick some up at the local Dollar Tree Store.

Drawer and shelf liner

At this point you should be nearly finished.  Turn on the shaker or rocker and make sure sure everything holds together.  If it all looks good I would place a drop of superglue onto each of the nuts holding the PVC end caps to the platform.  I reckon this ought to help prevent the nut from shaking loose.

Now you should be done.


If you have any questions, corrections, or comments please contact me.

Two tissue staining tools for 24-well culture plates.

June 29, 2011

This post highlights two simple tools I made to make tissue staining faster.  I was driven to create these devices after I had to drain and fill over 1000 wells one by one.  The tissue staining these tools are used for are of 300 micron thick coronal sections of embryonic mouse brains that are stored in  24-well plates.

Vacuum Suction Tool



The vacuum suction device can drain 4 wells of a 24-well plate at the same time. These plates are used for many things such as cell culture and tissue staining. Draining the wells of the plate one by one is quite laborious and so this make-shift device greatly reduces the time spent. Disposable pipette tips are placed over the ends of 6″ glass pasteur pipettes to help keep the device clean, vacuum suction keeps the tips on (though as you will see halfway through the video, a small piece of agarose clogged one tip and this caused a loss of suction which led to a tip coming off ).

The technique shown in the video is important in avoiding damage to the tissue and a description of it follows. The plate is held at an angle and the suction device drains fluid from the highest side of the wells. Gravity helps keep the tissue from floating towards the pipette tips. Next the plate is slowly brought level again and the rest of the fluid is removed. Since the level of the fluid is reduced before the plate is brought level, most tissue samples will not be able to be pulled towards the pipette – thus reducing the risk of damage.

How to make one

Materials:  6″ glass pipettes, 3/8″ vinyl tubing, 1/4″ vinyl tubing, hot-glue gun and hot-glue sticks, aquarium air-splitter( I do not know the real name for these), and an attachment substrate (I used the lids of Ikea brand plastic containers, though anything really should work).

How:  Use a 24-well plate as a guide to mark the substrate with a pen.  This is how you will establish the proper spacing for the pipettes.  Once you have the spacing marked, apply a few drops of hot glue and attach each glass pipette one after the other.  At this point the small amount of glue will be strong enough for you to check the spacing but not strong enough for active use.  Once you know the pipettes are spaced evenly horizontally and vertically add copious amounts of glue around and between the pipettes and then finish by adding a second substrate to the top (such that each substrate is like sandwich bread between some meat).

Cut four 1.5″ pieces of 3/8″ tubing and attach these on the ends of each glass pipette.  Next cut four 6″ pieces of 1/4″ tubing and then attach one end of these tubes to the aquarium-air splitter and push the other end of the tubes inside the 3/8″ tubing that is fixed to the pipettes.  Attach the aquarium air-splitter to whichever vacuum line you typically use for draining samples.

Well Filling Tool



When you have over a thousand wells that need to be quickly filled with solution the use of a 3mL plastic pipette simply sucks.  Originally I started using 50mL syringes because I did not have to refill them as often as the 3mL pipettes.  But as my mind wandered during the mindless filling of countless wells I decided I wanted a way to fill more than one at a time.  I had tubing and drip-system fittings laying around and so I decided to build something.

While I failed in my goal was to make something that filled all 24-wells at once, I did succeed at multiplying the number of wells that could be filled.  Ultimately the humongous size of the drip-system fittings prevented me from making a robust filling system because the spacing needed exceeded the size of the 24-well plate.

How to make one

Materials: 50mL syringe, 1/4″ tubing, 1/4″ drip system fittings (1 “T” intersection” and two right angle turn pieces), razor blade

How:  Some of the tips of the 1/4″ drip system fittings need to be truncated in order for them to align with the plate’s wells.  Cut the tips off the fittings as indicated by the red “*” in the figure below.  Use 1/4″ vinyl tubing to attach the fittings together with the tubes as indicated by the placement of blue lines in the figure below.  Lastly, use 1/4″ vinyl tubing to connect the fittings to the 50mL syringe, the placement is indicated by the green line in the figure below.

Note:  The right angle turn fittings will directly touch the T-intersection piece – the tubing merely holds them together.

Cell Spreader

April 15, 2011

Can’t find your cell spreader?  Too cheap to buy one?  Did someone indefinitely borrow yours?

Well, if you have access to a Bunsen burner and 9″ pasteur pipettes you can quickly make a spreader of your own.



Additional examples:


The video below shows how to warp the pipette with heat into the shape of a cell spreader.

More information:

  • First pass; place the pasteur pipette into the flame and after a few seconds the tip of the pipette will bend downwards via gravity.  This is because the heat weakens the glass and the portion of the pipette which is in the flame will act like a pivot point.
  • The pipette will very quickly cool and you can near immediately put it back into the flame.
  • Second pass; as before, put the pipette into the flame and it will bend downwards via gravity.
  • Third pass; place the very tip of the pipette into the flame and melt it shut.  If it is not closed off, the tip will fill up when you sterilize it with alcohol and will spark.