Below are some suggestions for efficient use of Adobe Illustrator which I’ve compiled over the years. May be handy at poster time. If anyone has any other tips please add them in the comments!

(on Mac, replace all “Control” with “Command (Apple) key”)

control-X “cut” cuts a selection out of a group!

different ways to “paste”: control-F (paste in front), control-B (paste in back), control-V (paste). control-F is especially useful in conjunction with above when you want to get an object out of a group, e.g. after selecting a piece of a group with the white arrow, ctrl-X to free it from its group, then ctrl-F to put it right back where it was. ctrl-V pasting, which is the normal paste shortcut from every other program, dumps the clipboard to the center of the screen, which can be useful also.

remove arrowheads by selecting the arrow, then clicking the triangle on the appearance palette and selecting “reduce to basic appearance”

Positions and sizes of objects can be specified numerically in the Transform palette. Rulers on sides of document (View > Show Rulers) determine the origin. Very handy for lining things up in posters, or making figures with similar layouts correspond nicely.

If rulers become offset by accident, you can reset the origin by double-clicking the top left corner where the horizontal and vertical rulers intersect.

For figures, to cut all the extra stuff which is outside of the margins before exporting to tiff, select the figure only, then do Select > Inverse to invert the selection, then delete.

if you make scale bars in Igor and then export eps to Illustrator, you have to remove the caps (Stroke palette) in order to get the accurate length.

control-0 (zero) zooms the artboard to match the window size (very handy after resizing a window on screen)
control-1 zooms the artboard to actual size (good for checking font sizes on a poster)

when you’re finished typing in a text box, control-clicking anywhere completes the text box and frees the cursor to do stuff outside the text box (like make another text box).

Most tools have a keyboard shortcut which selects them. The shortcuts are laid out in an intuitive way and it saves an enormous amount of time to learn them. If you hate the layout, they can be changed in the preferences. One tool which lacks a shortcut by default is the “white-arrow-plus” tool. I’ve found it useful to set that one to shift-A, since the white arrow by itself is A.

Preferences are your friend! Almost everything can be customized, including the distance that objects move when you arrow-key and shift-arrow-key, the spacing of grid lines, the units for size and position, etc.

arrowhead border bug in Illustrator 9 & 10:
In AI 9 and 10 there is a bug which causes an unsightly white border around arrowheads which is most annoying when they are placed on a colored background. you can avoid this by applying the arrowhead effect to the stroke only, instead of at the object level. To do this, select the object, open the Appearance palette, and drag the Add Arrowhead effect into the Stroke layer, instead of leaving it below both the Stroke and the Fill layers.

What is going on is when the effect is below both the fill and the stroke layers, it is applied to both the Fill and to the Stroke. But the filled object has no stroke weight and no stroke color, so the default stroke weight of 1 and default color of white are used.

In AI CS the Add Arrowhead effect ignores unpainted paths, so it won’t make this halo around unfilled paths, even when it is applied at the object level.

Never get lost in the woods again! An article in Wired describes how some Neuroscientists are trying to tap into our common senses to let us perceive uncommon things.

Wei Chen’s group has published a Neuron Techinques paper on their method to load small groups of neurons in vivo with dextran-conjugated fluorescent calcium indicators. As seen at SfN 2006. Link to article html or pdf

Also see Thomas Nevian and Fritjof Helmchen’s paper on cell electroporation here.

Here is a link to a very beautiful movie The Inner Life of a Cell. Those who has a degree in Molecular Biology will enjoy it a lot. Before downloading 24 Mb you may want to check some screen shots

A new combined modeling and physiology study from Santamaria, Tripp, and Bower offers a satisfying explanation for the decades-long failure to observe beam-like activation of Purkinje cells along parallel fibers in response to physiologically realistic granule cell activation. In rat Crus IIa, they find that beamlike patterns of Purkinje cells can be activated via granule cells by sensory stimuli, but only under bicuculline or gabazine. The modeling data predict that local basket cell inhibition and a spatial gradient of stellate cell inhibition contribute to the functional difference between ascending branch and parallel fiber pf-pc synapses, preventing beam-like responses under normal conditions. They further suggest that the primary effect of this local computation is to regulate the Purkinje cell’s dendritic voltage and calcium dynamics rather than its spike output. These observations support a model of cerebellar function in which parallel fiber synapses and molecular layer inhibition act at a distance to modulate the responsiveness of Purkinje cells to local ascending branch input.

pdf

A nice paper by Pijpers et al. showing the anatomical convergence of Mossy Fiber (MF) and Climbing Fiber (CF) inputs in the same zonal location. PDF.

Using small injections of cholera b toxin this paper demonstrates that mossy fiber collaterals terminate in the granule cell layer directly below labeled axon collaterals of climbing fibers. From this it is concluded that the mossy fiber system makes use of highly organized projection patterns that relate closely to the topography of the climbing fiber system.

A song about us ? Maybe!

A new paper out by the infamous duo of Jorntell and Ekerot.

This paper argues that granule cells (GC) are threshold detectors en lieu of sparse coders. In vivo patch clamp recordings of GC in this article also suggest that these cells receive inputs on their 3-5 dendrites from the same mossy fiber projections. (Also see the paper by Pijpers et al. above)

The Allen Brain Atlas is an interactive, genome-wide image database of gene expression in the mouse brain. A combination of RNA in situ hybridization data, detailed Reference Atlases and informatics analysis tools are integrated to provide a searchable digital atlas of gene expression. Together, these resources present a comprehensive online platform for exploration of the brain at the cellular and molecular level. Check it out!

Wikipedia has now a Neuroscience Portal.

The full German edition of this work can be downloaded as a searchable PDF from Google books.

EM tells you that the distance between two cells is in the range of 20 nm in fixed tissue. Thorne & Nicholson, however, find a much wider gap of 38-64 nm by looking at dye diffusion in vivo.

From the Callaway lab: Selective and Quickly Reversible Inactivation of Mammalian Neurons In Vivo Using the Drosophila Allatostatin Receptor. [html][pdf]

The insect allatostatin receptor (AlstR) is a G protein-coupled inward-rectifying K+ (GIRK) channel, that when binding its ligand can silence the neurons in which it is expressed.

Zeiss added several very helpful paged to its web portal. Click on ‘New: Filter sets & Objectives’. You can find there e.g. transmittance curves of objectives or spectra of dyes. A direct link can be found here.

There has been broad news coverage of this paper. The paper proposes that pain sensitivity increases more in mice that are visually exposed to their cage mates being presented noxious stimuli (acetic acid injections creating thermal hyperalgesia) than if these mice were exposed to unfamiliar animals.

David Linden’s group shows that long-term depression can be elicited at mossy fiber-deep cerebellar nucleus synapses with high-frequency burst stimulation, or through pairing with postsynaptic depolarization. Postsynaptic origin of this type of plasticity is supported by lack of changes to the paired pulse ratio and block of expression with a postsynaptic Ca²⁺ chelator. mGluR1, but not mGluR5 activation is required. [Link to article]

Institute for Advanced Study/Rita Allen Foundation symposium. Wednesday and Thursday. The speakers are Rita Allen Scholars, including me. Much of the focus of the other talks is cancer. For a schedule click here.

The Public Library of Science is introducing a new journal this year, PLoS ONE, www.plosone.org. It’s another example of experimentation with the standard publication model. The idea is to select papers of high technical quality, but not judge them one the basis of novelty or how interesting the work is. Instead, papers are rapidly published online, followed by an open and continuous review of the work in the debate forums.

Gayle’s learning rule paper. The CA3-CA1 synaptic learning rule paper is out at last! [Abstract] [PDF] I am excited about this paper because I feel that we have built bridges among three different approaches to understanding hippocampal plasticity: (1) spike-timing-dependent plasticity, which has been a contentious subject at this, the most-studied synapse of all; (2) several decades of slice plasticity experiments, which have been at times nominally contradictory; and (3) in vivo firing patterns, which have features that are reminiscent of the patterns we applied. I hope this paper will be a step toward synthesizing those bodies of knowledge.

A new Progress in Neurobiology review by Masao Ito has just become available online. It’s quite comprehensive, with some nice history.