I put leaf samples in the plastic seal bags, and freeze-dried, but the majority of the bags were broken and some samples were lost. Anyone have experience with this?
I don't have experience on plant management. However, adding glycerol to protein samples helps in minimizing effects of freezing and thawing. Although a different issue completely, it may be helpful to use glycerol in a way such as rubbing the plastic bags with glycerol or glycerin to prevent plastic breakage. You may want to give that a try on experimental samples. All the best
I've often used ziplock packets. Make sure you freeze the samples first before putting them in the freeze drier otherwise they may boil as the pressure drops and you want the ice in the samples to sublimate rather then boil which it will do if it is still a liquid. I've seen soil samples spew like a volcano as the pressure drops so i usually seal these in urine bottles with filter paper taped over the open jar to keep the soil in and let the water molecules out. Make sure the ziplocks are slightly open as no freeze drying will happen if the packets are still sealed - you would be surprised how many post-graduate students try and dry sealed samples :). They don't need to be open a lot, just enough for there to be a continuous space connection between the sample and the freeze drying space. How long to run them depends on the samples but i used to use a three-day program for bulk samples and a week for water hyacinth - it has some sort of mucilage that hinders the drying process. Essentially when the sample is brittle and breaks under your fingers, its dry. bare in mind though that if it isn't warmed to room temp when you take it out it will immediately start absorbing moisture out the atmosphere so seal it as soon as you can.
You can place your sample on a metalic tray in reasonable quantity.
You must be vigilant for preparing your sample about heat transfer and mass phenomena during freeze drying process.
From pratical point of view, your product must be well spread in quantity not very important to ensure a better transfer of heat and mass transfer (removal of water by sublimation). I recommend avoiding the use of bags.