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Update installation instructions for Macs, min version of rastermap #1009

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Update installation instructions for Macs, min version of rastermap #1009

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Update README.md
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Update setup.py
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32 changes: 15 additions & 17 deletions README.md
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Expand Up @@ -15,8 +15,8 @@
[![GitHub forks](https://img.shields.io/github/forks/MouseLand/suite2p?style=social)](https://github.com/MouseLand/suite2p/)


Pipeline for processing two-photon calcium imaging data.
Copyright (C) 2018 Howard Hughes Medical Institute Janelia Research Campus
Pipeline for processing two-photon calcium imaging data.
Copyright (C) 2018 Howard Hughes Medical Institute Janelia Research Campus

suite2p includes the following modules:

Expand All @@ -25,9 +25,9 @@ suite2p includes the following modules:
* Spike detection
* Visualization GUI

This code was written by Carsen Stringer and Marius Pachitariu.
This code was written by Carsen Stringer and Marius Pachitariu.
For support, please open an [issue](https://github.com/MouseLand/suite2p/issues).
The reference paper is [here](https://www.biorxiv.org/content/early/2017/07/20/061507).
The reference paper is [here](https://www.biorxiv.org/content/early/2017/07/20/061507).
The deconvolution algorithm is based on [this paper](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005423), with settings based on [this paper](http://www.jneurosci.org/content/early/2018/08/06/JNEUROSCI.3339-17.2018).

You can now run suite2p in google colab, no need to locally install: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MouseLand/suite2p/blob/main/jupyter/run_suite2p_colab_2021.ipynb). Note you do not have access to the GUI via google colab, but you can download the processed files and view them locally in the GUI.
Expand All @@ -54,14 +54,14 @@ Pachitariu, M., Stringer, C., Schröder, S., Dipoppa, M., Rossi, L. F., Carandin
2. Open an anaconda prompt / command prompt with `conda` for **python 3** in the path
3. Create a new environment with `conda create --name suite2p python=3.9`.
4. To activate this new environment, run `conda activate suite2p`
5. (Option 1) You can install the minimal version of suite2p, run `python -m pip install suite2p`.
5. (Option 1) You can install the minimal version of suite2p, run `python -m pip install suite2p`.
6. (Option 2) You can install the GUI version with `python -m pip install suite2p[gui]`. If you're on a zsh server, you may need to use `' '` around the suite2p[gui] call: `python -m pip install 'suite2p[gui]'`. This also installs the NWB dependencies.
7. Now run `python -m suite2p` and you're all set.
8. Running the command `suite2p --version` in the terminal will print the install version of suite2p.

For additional dependencies, like h5py, NWB, Scanbox, and server job support, use the command `python -m pip install suite2p[io]`.

If you are running suite2p on Windows or Linux we recommend installing ScanImage Tiff Reader with `pip install scanimage-tiff-reader` (this package is no longer supported on Mac, but may be supported again in the near future, we will change the instructions accordingly if so).
We recommend installing ScanImage Tiff Reader with `pip install scanimage-tiff-reader`.

If you have an older `suite2p` environment you can remove it with `conda env remove -n suite2p` before creating a new one.

Expand All @@ -73,11 +73,9 @@ pip install --upgrade suite2p
~~~~

### Installation for Macs with Apple Silicon chips (e.g., M1)
1. Download an iTerm2 terminal from this [link](https://iterm2.com/). Install it into your /Applications folder. If you already have downloaded iTerm, duplicate it and give it whatever name you'd like (e.g., "iterm2Rosetta").
2. Navigate to the iTerm app you will use, right click it, and then select "Get Info". Check "Open using Rosetta".
3. Open up this iTerm app and follow steps 1 & 2 in the installation section [above](#installation_section) to install anaconda.
4. Use the following command `CONDA_SUBDIR=osx-64 conda create --name suite2p python=3.9`
5. Follow steps 4-7 in the installation section [above](#installation_section) to install the `suite2p` package.
1. Follow steps 1 & 2 in the installation section [above](#installation_section) to install anaconda.
2. Use the following command `CONDA_SUBDIR=osx-64 conda create --name suite2p python=3.9`
3. Follow steps 4-7 in the installation section [above](#installation_section) to install the `suite2p` package.


### Installing the latest github version of the code
Expand All @@ -88,7 +86,7 @@ pip install git+https://github.com/MouseLand/suite2p.git
~~~

If you want to download and edit the code, and use that version,
1. Clone the repository with git and `cd suite2p`
1. Clone the repository with git and `cd suite2p`
2. Run `pip install -e .` in that folder

**Common issues**
Expand Down Expand Up @@ -148,7 +146,7 @@ The GUI serves two main functions:

Main GUI controls (works in all views):

1. Pan = Left-Click + drag
1. Pan = Left-Click + drag
2. Zoom = (Scroll wheel) OR (Right-Click + drag)
3. Full view = Double left-click OR escape key
4. Swap cell = Right-click on the cell
Expand All @@ -174,10 +172,10 @@ See our example jupyter notebook [here](jupyter/run_pipeline_tiffs_or_batch.ipyn
## Outputs

~~~~
F.npy: array of fluorescence traces (ROIs by timepoints)
Fneu.npy: array of neuropil fluorescence traces (ROIs by timepoints)
spks.npy: array of deconvolved traces (ROIs by timepoints)
stat.npy: array of statistics computed for each cell (ROIs by 1)
F.npy: array of fluorescence traces (ROIs by timepoints)
Fneu.npy: array of neuropil fluorescence traces (ROIs by timepoints)
spks.npy: array of deconvolved traces (ROIs by timepoints)
stat.npy: array of statistics computed for each cell (ROIs by 1)
ops.npy: options and intermediate outputs
iscell.npy: specifies whether an ROI is a cell, first column is 0/1, and second column is probability that the ROI is a cell based on the default classifier
~~~~
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2 changes: 1 addition & 1 deletion setup.py
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install_deps = ["importlib-metadata",
"natsort",
"rastermap>0.1.0",
"rastermap>=0.9.0",
"tifffile",
"torch>=1.13.1",
"numpy>=1.24.3",
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